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- PDB-2r5i: Pentamer Structure of Major Capsid Protein L1 of Human Papilloma ... -

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Basic information

Entry
Database: PDB / ID: 2r5i
TitlePentamer Structure of Major Capsid Protein L1 of Human Papilloma Virus type 18
ComponentsL1 protein
KeywordsVIRAL PROTEIN / HPV18 / pentamer / type specific epitope / capsid / Capsid protein / Virion
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / membrane
Similarity search - Function
Major capsid L1 (late) superfamily, Papillomavirus / Polyomavirus Vp1; Chain A / Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / 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 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBishop, B. / Dasgupta, J. / Chen, X.S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structures of four types of human papillomavirus L1 capsid proteins: understanding the specificity of neutralizing monoclonal antibodies.
Authors: Bishop, B. / Dasgupta, J. / Klein, M. / Garcea, R.L. / Christensen, N.D. / Zhao, R. / Chen, X.S.
History
DepositionSep 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L1 protein
B: L1 protein
C: L1 protein
D: L1 protein
E: L1 protein
F: L1 protein
G: L1 protein
H: L1 protein
I: L1 protein
J: L1 protein
K: L1 protein
L: L1 protein
M: L1 protein
N: L1 protein
O: L1 protein


Theoretical massNumber of molelcules
Total (without water)713,86815
Polymers713,86815
Non-polymers00
Water00
1
A: L1 protein
B: L1 protein
C: L1 protein
D: L1 protein
E: L1 protein


Theoretical massNumber of molelcules
Total (without water)237,9565
Polymers237,9565
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36990 Å2
MethodPISA
2
F: L1 protein
G: L1 protein
H: L1 protein
I: L1 protein
J: L1 protein


Theoretical massNumber of molelcules
Total (without water)237,9565
Polymers237,9565
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37200 Å2
MethodPISA
3
K: L1 protein
L: L1 protein
M: L1 protein
N: L1 protein
O: L1 protein


Theoretical massNumber of molelcules
Total (without water)237,9565
Polymers237,9565
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.161, 105.039, 235.749
Angle α, β, γ (deg.)87.56, 85.66, 68.16
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 20 - 475 / Label seq-ID: 1 - 428

Dom-IDAuth asym-IDLabel asym-ID
1AA
2OO

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Components

#1: Protein
L1 protein


Mass: 47591.188 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 18 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 18 / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80B70, UniProt: P06794*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.79 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 98881 / Redundancy: 3.55 % / Rsym value: 19.6 / Net I/σ(I): 4.4

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.856 / SU B: 30.746 / SU ML: 0.503 / Cross valid method: THROUGHOUT / ESU R Free: 0.657 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26016 4995 5.1 %RANDOM
Rwork0.21383 ---
obs0.21619 93692 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.199 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å2-2.84 Å2-0.97 Å2
2--6.31 Å2-2.11 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 3.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49845 0 0 0 49845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.02251120
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7611.9569525
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05356315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12324.4382400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.953158175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.34915255
X-RAY DIFFRACTIONr_chiral_restr0.1630.27500
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0239645
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2810.223191
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3540.235641
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.21496
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4060.2256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5151.532426
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.663251195
X-RAY DIFFRACTIONr_scbond_it4.875321865
X-RAY DIFFRACTIONr_scangle_it6.4924.518330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3323 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.165
loose thermal2.3210
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 345 -
Rwork0.26 6865 -
obs--99.6 %

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