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- PDB-1ihm: CRYSTAL STRUCTURE ANALYSIS OF NORWALK VIRUS CAPSID -

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Basic information

Entry
Database: PDB / ID: 1ihm
TitleCRYSTAL STRUCTURE ANALYSIS OF NORWALK VIRUS CAPSID
Componentscapsid proteinCapsid
KeywordsVIRUS / Beta-barrel / EF-Tu-LIKE domain caliciviridae / T=3 icosahedral capsid / Icosahedral virus
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 / Jelly Rolls - #20 / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein ...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 / Jelly Rolls - #20 / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Jelly Rolls / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Icosahedral averaging / Resolution: 3.4 Å
AuthorsPrasad, B.V. / Hardy, M.E. / Dokland, T. / Bella, J. / Rossmann, M.G. / Estes, M.K.
CitationJournal: Science / Year: 1999
Title: X-ray crystallographic structure of the Norwalk virus capsid
Authors: Prasad, B.V. / Hardy, M.E. / Dokland, T. / Bella, J. / Rossmann, M.G. / Estes, M.K.
History
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[2] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: capsid protein
B: capsid protein
C: capsid protein


Theoretical massNumber of molelcules
Total (without water)169,8893
Polymers169,8893
Non-polymers00
Water0
1
A: capsid protein
B: capsid protein
C: capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,193,369180
Polymers10,193,369180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: capsid protein
B: capsid protein
C: capsid protein
x 5


  • icosahedral pentamer
  • 849 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)849,44715
Polymers849,44715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: capsid protein
B: capsid protein
C: capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.02 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,019,33718
Polymers1,019,33718
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: capsid protein
B: capsid protein
C: capsid protein
x 30


  • crystal asymmetric unit, crystal frame
  • 5.1 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)5,096,68590
Polymers5,096,68590
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)605.740, 605.740, 466.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.56583756, 0.22498171, -0.79304862), (-0.73862848, 0.56584319, -0.36632478), (0.36648527, 0.79340392, 0.48635323)32.04474, 179.66091, -177.68534
3generate(-0.13664638, -0.37460043, -0.91685485), (-0.97014427, -0.1366429, 0.20032267), (-0.20041831, 0.91726925, -0.34474469)231.51039, 322.7422, -109.81558
4generate(-0.1366429, -0.97014427, -0.20032267), (-0.37460043, -0.13664638, 0.91685485), (-0.91726925, 0.20041831, -0.34474469)322.7422, 231.51039, 109.81558
5generate(0.56584319, -0.73862848, 0.36632478), (0.22498171, 0.56583756, 0.79304862), (-0.79340392, -0.36648527, 0.48635323)179.66091, 32.04474, 177.68534
6generate(0.73111214, -0.41539456, -0.54109715), (-0.41539503, -0.90032255, 0.12984085), (-0.54134859, 0.12990105, -0.83078959)104.82635, 354.7486, 63.03033
7generate(0.52220884, -0.49986993, -0.69080251), (0.47754252, -0.49988143, 0.72238744), (-0.70673612, -0.70744164, -0.02232741)149.76952, 156.61378, 216.64023
8generate(0.4115346, -0.71344598, -0.56699629), (0.90418251, 0.39772886, 0.15573999), (0.11445603, -0.57701839, 0.80877051)199.44195, -46.2503, 70.86069
9generate(0.55203747, -0.76096788, -0.34077449), (0.27492298, 0.55204141, -0.78701399), (0.78736821, 0.34093028, 0.5139551)185.19804, 26.50761, -172.84591
10generate(0.74954726, -0.57676197, -0.32476794), (-0.54062079, -0.25019848, -0.80302054), (0.38205867, 0.77783052, -0.49934877)126.72239, 274.33856, -177.68534
11generate(-0.76096788, 0.55203747, 0.34077449), (0.55204141, 0.27492298, 0.78701399), (0.34093028, 0.78736821, -0.5139551)185.19804, 26.50761, -172.84591
12generate(-0.71344598, 0.4115346, 0.56699629), (0.39772886, 0.90418251, -0.15573999), (-0.57701839, 0.11445603, -0.80877051)199.44195, -46.2503, 70.86069
13generate(-0.49986993, 0.52220884, 0.69080251), (-0.49988143, 0.47754252, -0.72238744), (-0.70744164, -0.70673612, 0.02232741)149.76952, 156.61378, 216.64023
14generate(-0.41539456, 0.73111214, 0.54109715), (-0.90032255, -0.41539503, -0.12984085), (0.12990105, -0.54134859, 0.83078959)104.82635, 354.7486, 63.03033
15generate(-0.57676197, 0.74954726, 0.32476794), (-0.25019848, -0.54062079, 0.80302054), (0.77783052, 0.38205867, 0.49934877)126.72239, 274.33856, -177.68534
16generate(-0.2502051, -0.57675929, -0.77747814), (-0.5406198, 0.74955021, -0.38189526), (0.80337764, 0.32492085, -0.4993451)279.87569, 121.18526, -172.84591
17generate(-0.00049889, -0.99950111, 0.03157703), (-0.99950111, -0.00049889, -0.03157703), (0.03158283, -0.03158283, -0.99900221)306.3833, 306.3833
18generate(0.74955021, -0.5406198, 0.38189526), (-0.57675929, -0.2502051, 0.77747814), (-0.32492085, -0.80337764, -0.4993451)121.18526, 279.87569, 172.84591
19generate(0.96339982, 0.16572626, -0.21065133), (0.14339082, 0.34551707, 0.9271835), (0.22654256, -0.92386938, 0.30911707)-19.78104, 78.29504, 106.82465
20generate(0.34551707, 0.14339082, -0.9271835), (0.16572626, 0.96339982, 0.21065133), (0.92386938, -0.22654256, 0.30911707)78.29504, -19.78104, -106.82465
21generate(0.47754166, 0.52220802, 0.70641911), (-0.49987466, -0.49987502, 0.70712468), (0.72270842, -0.69111773, 0.02233335)0.03835, 306.34495, -4.83943
22generate(0.14338549, 0.96340168, -0.22644228), (0.34552484, 0.16572196, 0.9234539), (0.92759965, -0.21074871, -0.30910747)-16.3589, 74.87291, -109.81558
23generate(-0.71345078, 0.3977332, -0.57676052), (0.41153621, 0.90418136, 0.11439873), (0.5672524, -0.15580485, -0.80876457)201.55695, -48.3653, -63.03033
24generate(-0.90884855, -0.39306282, 0.1395923), (-0.39306601, 0.69497738, -0.60195409), (0.13965432, -0.60221668, -0.78612882)352.6336, 106.94135, 70.86069
25generate(-0.17277474, -0.31613315, 0.93264092), (-0.9563489, -0.17277718, -0.2356293), (0.23573142, -0.93305824, -0.27248206)228.08826, 326.16434, 106.82465
26generate(-0.39306282, -0.90884855, -0.1395923), (0.69497738, -0.39306601, 0.60195409), (-0.60221668, 0.13965432, 0.78612882)352.6336, 106.94135, 70.86069
27generate(0.3977332, -0.71345078, 0.57676052), (0.90418136, 0.41153621, -0.11439873), (-0.15580485, 0.5672524, 0.80876457)201.55695, -48.3653, -63.03033
28generate(0.96340168, 0.14338549, 0.22644228), (0.16572196, 0.34552484, -0.9234539), (-0.21074871, 0.92759965, 0.30910747)-16.3589, 74.87291, -109.81558
29generate(0.52220802, 0.47754166, -0.70641911), (-0.49987502, -0.49987466, -0.70712468), (-0.69111773, 0.72270842, -0.02233335)0.03835, 306.34495, -4.83943
30generate(-0.31613315, -0.17277474, -0.93264092), (-0.17277718, -0.9563489, 0.2356293), (-0.93305824, 0.23573142, 0.27248206)228.08826, 326.16434, 106.82465

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Components

#1: Protein capsid protein / Capsid


Mass: 56629.828 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Genus: Norovirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q83884

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 50

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Sample preparation

Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Ammonium dihydrogen phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.5 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.908 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 3.2→35 Å / Num. all: 685316 / Num. obs: 1370632 / % possible obs: 50 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.126
Reflection
*PLUS
Num. obs: 685316 / Num. measured all: 1370632
Reflection shell
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 5 Å / % possible obs: 54 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1refinement
RefinementMethod to determine structure: Icosahedral averaging
Starting model: Cryo-EM structure of the capsid at 20 Angstroms resolution

Resolution: 3.4→35 Å / σ(F): 1 /
RfactorNum. reflection
all0.26 685316
obs0.26 485000
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 3.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11284 0 0 0 11284
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.468
X-RAY DIFFRACTIONx_dihedral_angle_d26.382
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: parhcsdx.pro / Topol file: tophcsdx.pro
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 35 Å / σ(F): 1 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.382
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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