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- PDB-1dzl: L1 protein of human papillomavirus 16 -

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Basic information

Entry
Database: PDB / ID: 1dzl
TitleL1 protein of human papillomavirus 16
ComponentsLATE MAJOR CAPSID PROTEIN L1
KeywordsVIRUS / ICOSAHEDRAL
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Major capsid L1 (late) superfamily, Papillomavirus / Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Polyomavirus Vp1; Chain A / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major capsid protein L1 / Major capsid protein L1
Similarity search - Component
Biological speciesHUMAN PAPILLOMAVIRUS TYPE 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 3.5 Å
AuthorsChen, X.J. / Garcea, B. / Goldberge, I. / Harrison, S.C.
CitationJournal: Mol.Cell / Year: 2000
Title: Structure of Small Virus-Like Particles Assembled from the L1 Protein of Human Papillomavirus 16
Authors: Chen, X.J. / Garcea, B. / Goldberg, I. / Casini, G. / Harrison, S.C.
History
DepositionMar 1, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. RESIDUES 360 ... SHEET DETERMINATION METHOD: DSSP THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. RESIDUES 360 TO 382 FORM A CONTINIOUS STRAND THAT CONTRIBUTES TO A COMPLEX SHEET ARRANGEMENT. THIS HAS BEEN REPRESENTED HERE AS THREE SHEETS EACH CONTAINING A STRAND THAT IS A FRAGMENT OF THIS LONG 23 RESIDUE STRAND. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, THREE SHEETS ARE DEFINED, SHEETS A, A1 AND A2 WHERE STRANDS A (2), A1 (2) AND A2 (2) ARE PARTS OF THE SINGLE STRAND FOR RESIDUES 360 TO 382.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LATE MAJOR CAPSID PROTEIN L1


Theoretical massNumber of molelcules
Total (without water)56,4411
Polymers56,4411
Non-polymers00
Water00
1
A: LATE MAJOR CAPSID PROTEIN L1
x 60


Theoretical massNumber of molelcules
Total (without water)3,386,46760
Polymers3,386,46760
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: LATE MAJOR CAPSID PROTEIN L1
x 5


  • icosahedral pentamer
  • 282 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)282,2065
Polymers282,2065
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: LATE MAJOR CAPSID PROTEIN L1
x 6


  • icosahedral 23 hexamer
  • 339 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)338,6476
Polymers338,6476
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: LATE MAJOR CAPSID PROTEIN L1
x 20


  • crystal asymmetric unit, crystal frame
  • 1.13 MDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)1,128,82220
Polymers1,128,82220
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)387.000, 387.000, 387.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.638182, 0.19873, -0.743794), (-0.714941, 0.511403, -0.476787), (0.285627, 0.836046, 0.468449)0.50497, 0.92565, -0.31733
3generate(0.052749, -0.393389, -0.917858), (-0.958069, -0.279163, 0.064588), (-0.281641, 0.875964, -0.391619)1.24722, 1.1893, 0.45213
4generate(0.052749, -0.958069, -0.281641), (-0.393389, -0.279163, 0.875964), (-0.917858, 0.064588, -0.391619)1.20098, 0.4266, 1.24501
5generate(0.638182, -0.714941, 0.285627), (0.19873, 0.511403, 0.836046), (-0.743794, -0.476787, 0.468449)0.43016, -0.30843, 0.96558
6generate(-0.059867, -0.997146, 0.045998), (-0.997146, 0.057616, -0.048788), (0.045998, -0.048788, -0.997749)1.12194, 1.10476, 1.0182
7generate(0.687833, -0.483384, 0.541503), (-0.691488, -0.209487, 0.691346), (-0.220748, -0.849974, -0.478346)0.15411, 0.67004, 1.31288
8generate(0.939222, 0.34221, -0.027469), (-0.094058, 0.333445, 0.938066), (0.330175, -0.878468, 0.345367)-0.11784, -0.09243, 0.56643
9generate(0.346888, 0.338694, -0.874617), (-0.030483, 0.936099, 0.350413), (0.937411, -0.094893, 0.335046)0.68192, -0.12896, -0.18959
10generate(-0.270582, -0.489074, -0.829212), (-0.588623, 0.765627, -0.259496), (0.76178, 0.417878, -0.495045)1.44815, 0.61095, 0.08962
11generate(-0.481921, 0.47276, -0.737733), (-0.710539, 0.281821, 0.644756), (0.512724, 0.83491, 0.200099)1.05555, 0.46255, -0.31918
12generate(-0.856265, -0.47078, -0.212546), (-0.47078, 0.541964, 0.696162), (-0.212546, 0.696162, -0.685699)1.48391, 0.16002, 0.64906
13generate(-0.270582, -0.588623, 0.76178), (-0.489074, 0.765627, 0.417878), (-0.829212, -0.259496, -0.495045)0.68319, 0.20304, 1.40372
14generate(0.465734, 0.282087, 0.83876), (-0.74014, 0.643715, 0.194483), (-0.485062, -0.711377, 0.508584)-0.24004, 0.53217, 0.90189
15generate(0.33512, 0.938058, -0.08799), (-0.877013, 0.344707, 0.334702), (0.3443, -0.034997, 0.938207)-0.00991, 0.69255, -0.16293
16generate(0.760947, -0.270915, -0.589546), (0.414592, -0.495907, 0.763013), (-0.499072, -0.825034, -0.26504)0.58283, 0.09445, 1.36265
17generate(0.510921, -0.480211, -0.712991), (0.837067, 0.466698, 0.285504), (0.195649, -0.742691, 0.640415)0.90339, -0.39736, 0.43105
18generate(0.465734, -0.74014, -0.485062), (0.282087, 0.643715, -0.711377), (0.83876, 0.194483, 0.508584)0.94314, 0.36673, -0.36085
19generate(0.687833, -0.691488, -0.220748), (-0.483384, -0.209487, -0.849974), (0.541503, 0.691346, -0.478346)0.64714, 1.33077, 0.08133
20generate(0.870285, -0.401491, -0.285323), (-0.401491, -0.913812, 0.06125), (-0.285323, 0.06125, -0.956472)0.42446, 1.16249, 1.14651

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Components

#1: Protein LATE MAJOR CAPSID PROTEIN L1


Mass: 56441.109 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN PAPILLOMAVIRUS TYPE 16 / Description: ISOLATED FROM CONDYLOMA ACUMINATUM TISSUE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9WPH4, UniProt: P03101*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growpH: 4.5 / Details: pH 4.50
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 %PEG11
20.2 M11NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→70 Å / Num. obs: 202000 / % possible obs: 89 % / Observed criterion σ(I): 1.5 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Rsym value: 0.12
Reflection
*PLUS
% possible obs: 87.5 % / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 3.62 Å / % possible obs: 56 % / Rmerge(I) obs: 0.41

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Processing

Software
NameClassification
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: SIR / Resolution: 3.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 1.5
RfactorNum. reflection% reflection
Rfree0.29 --
Rwork0.28 --
obs0.28 200000 89 %
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 0 0 3578
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.283 / Rfactor Rfree: 0.291
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 3.6 Å / Rfactor Rfree: 0.365 / Rfactor Rwork: 0.352 / Rfactor obs: 0.352

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