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- PDB-6h72: GI.1 human norovirus protruding domain in complex with Nano-94 an... -

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Basic information

Entry
Database: PDB / ID: 6h72
TitleGI.1 human norovirus protruding domain in complex with Nano-94 and 2-fucosyllactose (2FL)
Components
  • Capsid protein VP1
  • Nanobody (VHH) Nano-94
KeywordsVIRAL PROTEIN / Norovirus / GI.1 / P domain / Nano-94 / 2-fucosyllactose
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
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 speciesNorwalk virus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKilic, T. / Hansman, G.S.
CitationJournal: J. Virol. / Year: 2019
Title: Structural Basis of Nanobodies Targeting the Prototype Norovirus.
Authors: Ruoff, K. / Kilic, T. / Devant, J. / Koromyslova, A. / Ringel, A. / Hempelmann, A. / Geiss, C. / Graf, J. / Haas, M. / Roggenbach, I. / Hansman, G.
History
DepositionJul 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation_author.identifier_ORCID
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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Nanobody (VHH) Nano-94
D: Nanobody (VHH) Nano-94
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3248
Polymers92,2234
Non-polymers1,1014
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-7 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.650, 112.310, 121.350
Angle α, β, γ (deg.)90.00, 99.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Capsid protein VP1 / CP / p59


Mass: 31182.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus (strain GI/Human/United States/Norwalk/1968)
Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83884
#2: Antibody Nanobody (VHH) Nano-94


Mass: 14928.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Alpaca / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.5) and 20% (w/v) PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→49.35 Å / Num. obs: 54228 / % possible obs: 96.29 % / Redundancy: 2.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.07156 / Rpim(I) all: 0.05117 / Rrim(I) all: 0.08839 / Net I/σ(I): 9.99
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.4491 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 5273 / CC1/2: 0.736 / Rpim(I) all: 0.327 / Rrim(I) all: 0.5583 / % possible all: 94.35

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSVERSION Nov 1, 2016data reduction
XSCALEVERSION Nov 1, 2016data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZL5

2zl5


Resolution: 2.3→49.35 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.84
RfactorNum. reflection% reflection
Rfree0.2024 2712 5 %
Rwork0.1723 --
obs0.1738 54210 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6117 0 74 317 6508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036378
X-RAY DIFFRACTIONf_angle_d0.6988746
X-RAY DIFFRACTIONf_dihedral_angle_d4.8554144
X-RAY DIFFRACTIONf_chiral_restr0.049987
X-RAY DIFFRACTIONf_plane_restr0.0051139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2972-2.3390.3241370.27732595X-RAY DIFFRACTION93
2.339-2.3840.30811410.26112687X-RAY DIFFRACTION96
2.384-2.43260.321460.25422758X-RAY DIFFRACTION98
2.4326-2.48550.27921440.24362735X-RAY DIFFRACTION98
2.4855-2.54330.28411470.232805X-RAY DIFFRACTION98
2.5433-2.60690.26661430.22222703X-RAY DIFFRACTION98
2.6069-2.67740.28031420.21492711X-RAY DIFFRACTION97
2.6774-2.75620.25591450.2152756X-RAY DIFFRACTION97
2.7562-2.84510.25511420.20152682X-RAY DIFFRACTION96
2.8451-2.94680.2151440.19762751X-RAY DIFFRACTION97
2.9468-3.06480.24611450.19282754X-RAY DIFFRACTION98
3.0648-3.20430.19851450.1912746X-RAY DIFFRACTION97
3.2043-3.37320.20221420.1782699X-RAY DIFFRACTION97
3.3732-3.58440.20641420.17442704X-RAY DIFFRACTION96
3.5844-3.86110.18191410.16132678X-RAY DIFFRACTION95
3.8611-4.24950.1521430.1352716X-RAY DIFFRACTION96
4.2495-4.86390.14991430.1152709X-RAY DIFFRACTION95
4.8639-6.12620.15921400.13712660X-RAY DIFFRACTION93
6.1262-49.3650.16841400.15152649X-RAY DIFFRACTION92
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)
13.93360.97150.19379.4673-54.80050.0362-0.0542-0.18730.1774-0.3694-0.8770.05030.71950.30140.38210.13470.05580.4049-0.03970.408789.3941-22.7333147.3115
23.00062.94120.51733.623-0.74562.1411-0.43730.04710.4105-1.11070.48450.69570.13420.12430.00010.53980.0396-0.03360.41540.10840.471663.995838.1297119.0931
31.08721.69110.74824.81361.51781.681-0.21340.17510.0629-0.69540.49230.47210.1670.0518-0.25920.6715-0.016-0.18360.59120.12850.528257.046719.5549122.8732
49.13515.25583.12878.2313-0.21188.95940.35580.04510.08090.7386-0.2421-0.8251-0.2580.8503-0.16520.50780.0544-0.09950.4522-0.00330.655269.187736.0619129.7602
58.79433.7786-2.52082.88470.93937.23050.4065-0.91620.03051.6386-0.44741.2440.2676-0.63070.06280.62270.07270.11190.5330.05980.672956.315934.2605131.6434
61.65741.2554-0.54035.9059-3.13291.7861-0.0068-0.08880.55480.3790.06620.4058-0.2984-0.1821-0.07820.41320.0789-0.04620.37130.03320.454962.306834.588126.1848
71.08790.20250.07584.0042.94835.6120.2011-0.09440.0220.645-0.0047-0.05450.4610.4771-0.1780.4348-0.003-0.04070.4240.04420.327583.49150.0779192.0738
86.41190.2214-0.59632.82750.08854.08350.14050.490.29130.10940.0582-0.2491-0.09810.4991-0.19870.4003-0.0560.0090.5163-0.0210.334585.462910.3226186.1884
92.95020.89750.18514.10013.46595.19580.0969-0.13660.03760.08930.249-0.31910.10460.7076-0.35410.4399-0.0231-0.02120.43090.01270.341886.8846.5502191.0565
101.3740.3141-0.09845.44143.79375.45290.1549-0.0031-0.00890.2997-0.14890.13450.6359-0.2224-0.01230.39590.0389-0.04470.33540.02510.326979.37230.2204183.7295
111.18681.67010.28723.4252-1.63685.14320.00250.07030.00720.02240.02110.0205-0.0433-0.1049-0.02440.18970.01490.00750.2496-0.02490.261258.8762-4.9953138.7394
121.17710.47480.26671.58420.13321.38250.00760.1318-0.0061-0.11310.0014-0.0351-0.0408-0.0156-0.00580.28740.03430.00570.28330.01430.263766.06073.1994137.0039
132.84540.58730.81962.88121.71098.84740.12470.00030.013-0.0285-0.10180.50490.0026-0.9032-0.03860.3159-0.0726-0.020.3766-0.02160.448147.798-13.0963135.5516
141.2129-0.2372-0.32042.88520.13574.57170.0638-0.037-0.06050.078-0.0263-0.11440.04640.1461-0.04790.27610.0529-0.02530.24410.01260.295580.1455-12.8383151.5235
152.4395-3.3386-2.17965.75264.11385.0061-0.1239-0.2529-0.24680.55580.0960.26220.3414-0.25060.02250.3032-0.0380.00830.36830.0550.303864.8736-6.2196161.1917
162.2596-1.13150.33521.9976-0.77922.9571-0.0961-0.18610.11020.18630.0178-0.1086-0.3013-0.04910.10710.3542-0.0042-0.01420.262-0.01910.257572.51625.5054164.3051
173.0515-1.68171.90524.37362.7795.6422-0.1699-0.4717-0.11330.76180.0637-0.02980.6652-0.04690.13160.48540.058-0.0320.37480.02920.370877.6616-8.3139169.8394
181.0603-0.34260.13893.14330.13051.30030.05910.0658-0.20260.1097-0.0305-0.10350.32510.1875-0.03660.36960.0608-0.0150.34810.01540.327981.4848-17.6334151.108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 484 through 518 )
2X-RAY DIFFRACTION2chain 'C' and (resid 1 through 25 )
3X-RAY DIFFRACTION3chain 'C' and (resid 26 through 33 )
4X-RAY DIFFRACTION4chain 'C' and (resid 34 through 45 )
5X-RAY DIFFRACTION5chain 'C' and (resid 46 through 59 )
6X-RAY DIFFRACTION6chain 'C' and (resid 60 through 121 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 33 )
8X-RAY DIFFRACTION8chain 'D' and (resid 34 through 63 )
9X-RAY DIFFRACTION9chain 'D' and (resid 64 through 100 )
10X-RAY DIFFRACTION10chain 'D' and (resid 101 through 120 )
11X-RAY DIFFRACTION11chain 'A' and (resid 229 through 269 )
12X-RAY DIFFRACTION12chain 'A' and (resid 270 through 484 )
13X-RAY DIFFRACTION13chain 'A' and (resid 485 through 518 )
14X-RAY DIFFRACTION14chain 'B' and (resid 229 through 269 )
15X-RAY DIFFRACTION15chain 'B' and (resid 270 through 321 )
16X-RAY DIFFRACTION16chain 'B' and (resid 322 through 387 )
17X-RAY DIFFRACTION17chain 'B' and (resid 388 through 403 )
18X-RAY DIFFRACTION18chain 'B' and (resid 404 through 483 )

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