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- PDB-4x0c: Crystal structure of P domain from norovirus strain NSW0514 in co... -

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Basic information

Entry
Database: PDB / ID: 4x0c
TitleCrystal structure of P domain from norovirus strain NSW0514 in complex with HBGA type Lex (triglycan)
ComponentsVP1
KeywordsVIRAL PROTEIN / Viral capsid protein / 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
Lewis X antigen, alpha anomer / FORMIC ACID / VP1
Similarity search - Component
Biological speciesNorovirus Hu/GII.4/Sydney/NSW0514/2012/AU
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Human noroviruses' fondness for histo-blood group antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionNov 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 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 / entity_name_com / 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_molecule_features / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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 / 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_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_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)69,70514
Polymers68,1222
Non-polymers1,58312
Water13,457747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint25 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.830, 104.830, 191.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
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
1LYSLYSchain AAA225 - 5302 - 307
2SERSERchain BBB224 - 5301 - 307
Detailsbiological unit is the same as asym.

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Components

#1: Protein VP1


Mass: 34060.961 Da / Num. of mol.: 2 / Fragment: P DOMAIN, UNP residues 225-530
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: K4LM89
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis X antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis X antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978196 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978196 Å / Relative weight: 1
ReflectionResolution: 1.7→45.95 Å / Num. obs: 116084 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 20.39 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.08 / Χ2: 0.934 / Net I/σ(I): 15.62 / Num. measured all: 421454
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.753.60.4721.2861.229113852083191.51397.6
1.75-1.790.6341.0471.630331831482261.22298.9
1.79-1.850.7480.7612.1329756812380630.88999.3
1.85-1.90.8050.6172.5728833786378080.7299.3
1.9-1.960.8640.4623.4127788761875620.5499.3
1.96-2.030.9130.3344.627102741273650.3999.4
2.03-2.110.9430.2685.7825458712970390.31498.7
2.11-2.20.9660.1967.5425167689168630.22999.6
2.2-2.290.980.1489.6224151661865870.17399.5
2.29-2.410.9880.11312.1723205632963120.13299.7
2.41-2.540.9920.09513.9822138604660340.11199.8
2.54-2.690.9950.07317.5720973574057260.08599.8
2.69-2.880.9970.05521.9119629537153630.06599.9
2.88-3.110.9980.04127.6118368504950470.048100
3.11-3.40.9990.0336.7816817466846550.03599.7
3.4-3.80.9990.0244614947422342120.02899.7
3.8-4.390.9990.01855.7213057378437590.02299.3
4.39-5.3810.01563.1211279322532090.01899.5
5.38-7.6110.01659.078927255525460.01999.6
7.6110.01365.594415153413890.01690.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.67 Å45.95 Å
Translation4.67 Å45.95 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOS

4oos


Resolution: 1.72→40.142 Å / FOM work R set: 0.8872 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1795 5621 5 %
Rwork0.1596 106840 -
obs0.1606 112461 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.37 Å2 / Biso mean: 25.16 Å2 / Biso min: 10.59 Å2
Refinement stepCycle: final / Resolution: 1.72→40.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 142 747 5666
Biso mean--42.47 34.68 -
Num. residues----613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115086
X-RAY DIFFRACTIONf_angle_d1.2976938
X-RAY DIFFRACTIONf_chiral_restr0.054784
X-RAY DIFFRACTIONf_plane_restr0.007905
X-RAY DIFFRACTIONf_dihedral_angle_d12.4621874
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2783X-RAY DIFFRACTION5.005TORSIONAL
12B2783X-RAY DIFFRACTION5.005TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.73950.32081840.29983494X-RAY DIFFRACTION99
1.7395-1.760.29351830.29253487X-RAY DIFFRACTION99
1.76-1.78150.30241840.2773492X-RAY DIFFRACTION99
1.7815-1.8040.2851860.25933532X-RAY DIFFRACTION99
1.804-1.82780.25641840.24343485X-RAY DIFFRACTION99
1.8278-1.85280.2121840.22963524X-RAY DIFFRACTION99
1.8528-1.87930.25391860.22063529X-RAY DIFFRACTION99
1.8793-1.90730.25081850.22053513X-RAY DIFFRACTION99
1.9073-1.93710.2541850.22093513X-RAY DIFFRACTION99
1.9371-1.96890.22651850.19853521X-RAY DIFFRACTION99
1.9689-2.00280.20981860.1993531X-RAY DIFFRACTION100
2.0028-2.03930.21031840.18653501X-RAY DIFFRACTION99
2.0393-2.07850.221840.20083490X-RAY DIFFRACTION98
2.0785-2.12090.19141870.16833546X-RAY DIFFRACTION100
2.1209-2.1670.19131860.16483534X-RAY DIFFRACTION100
2.167-2.21740.171870.15463563X-RAY DIFFRACTION100
2.2174-2.27290.14941880.1373559X-RAY DIFFRACTION100
2.2729-2.33430.1591870.13493553X-RAY DIFFRACTION100
2.3343-2.4030.16521870.13273550X-RAY DIFFRACTION100
2.403-2.48050.16061880.13743573X-RAY DIFFRACTION100
2.4805-2.56920.15561870.13733578X-RAY DIFFRACTION100
2.5692-2.6720.17961880.13993568X-RAY DIFFRACTION100
2.672-2.79360.15871900.1383611X-RAY DIFFRACTION100
2.7936-2.94090.17021880.14683584X-RAY DIFFRACTION100
2.9409-3.1250.15931900.15373608X-RAY DIFFRACTION100
3.125-3.36620.16711900.1463625X-RAY DIFFRACTION100
3.3662-3.70480.19711910.15613633X-RAY DIFFRACTION100
3.7048-4.24030.14771920.13513665X-RAY DIFFRACTION100
4.2403-5.34040.13351940.11813690X-RAY DIFFRACTION99
5.3404-40.140.16452010.15953788X-RAY DIFFRACTION97
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)
11.64420.02380.26391.89440.11291.2079-0.0123-0.13890.0014-0.00990.0136-0.09440.10110.0121-0.01490.09690.01460.00890.13770.00720.1-22.094523.0384-24.4062
21.15570.69670.15992.5652-0.48040.7014-0.0556-0.07740.34050.0303-0.01150.3523-0.1318-0.31360.01810.12920.0744-0.00350.2518-0.04760.256-33.742741.1308-22.7905
30.95640.41210.30061.48550.3881.35790.1017-0.1681-0.18450.18-0.033-0.17420.3320.028-0.01410.1780.0315-0.01880.16770.04250.1673-20.654916.0914-20.1734
40.90710.23360.50010.48920.31231.9893-0.0203-0.00260.018-0.0048-0.0084-0.0453-0.04750.02030.03070.10740.0297-0.01320.13240.01250.1476-8.62336.882-32.8165
52.40380.4804-0.48170.2562-0.17852.28450.0138-0.2458-0.01790.0997-0.0796-0.0519-0.08920.04140.06250.12720.0156-0.02730.1493-0.01910.1304-7.464540.484-12.9479
61.50120.3568-0.11661.0549-0.51242.18010.0268-0.20870.23550.1257-0.03950.0385-0.33610.0877-0.00280.17010.0156-0.0330.143-0.03820.1733-6.923948.189-18.1159
70.6892-0.0798-0.00891.03140.27831.6403-0.03440.15220.0142-0.1958-0.0147-0.004-0.07070.06830.04890.13560.0219-0.0170.17450.02870.142-9.906737.3232-45.6678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 292 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 293 through 380 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 530 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 224 through 292 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 293 through 352 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 353 through 418 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 419 through 530 )B0

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