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- PDB-2r5j: Pentamer Structure of Major Capsid protein L1 of Human Papilloma ... -

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Basic information

Entry
Database: PDB / ID: 2r5j
TitlePentamer Structure of Major Capsid protein L1 of Human Papilloma Virus Type 35
ComponentsMajor capsid protein L1
KeywordsVIRAL PROTEIN / HPV35 / Capsid / Pentamer / Type specific epitope / Capsid protein / Late protein / Virion
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
Similarity search - Component
Biological speciesHuman papillomavirus type 35
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1
G: Major capsid protein L1
H: Major capsid protein L1
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
O: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)708,46615
Polymers708,46615
Non-polymers00
Water0
1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)236,1555
Polymers236,1555
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34320 Å2
ΔGint-195.9 kcal/mol
Surface area77640 Å2
MethodPISA
2
F: Major capsid protein L1
G: Major capsid protein L1
H: Major capsid protein L1
I: Major capsid protein L1
J: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)236,1555
Polymers236,1555
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34160 Å2
ΔGint-195.8 kcal/mol
Surface area77800 Å2
MethodPISA
3
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
O: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)236,1555
Polymers236,1555
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34550 Å2
ΔGint-201.9 kcal/mol
Surface area77600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.410, 176.606, 197.073
Angle α, β, γ (deg.)90.00, 92.11, 90.00
Int Tables number4
Space group name H-MP1211
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 - 474 / Label seq-ID: 1 - 423

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

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Components

#1: Protein
Major capsid protein L1


Mass: 47231.066 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 35 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 16 / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: P27232

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.68 %

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Data collection

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: 3.3→50 Å / Num. obs: 119918 / Redundancy: 6.19 % / Rsym value: 18.9 / Net I/σ(I): 2.6

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→15 Å / Cor.coef. Fo:Fc: 0.802 / Cor.coef. Fo:Fc free: 0.769 / SU B: 40.368 / SU ML: 0.676 / Cross valid method: THROUGHOUT / ESU R Free: 0.707 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34818 7364 5 %RANDOM
Rwork0.31549 ---
obs0.31715 119918 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.764 Å2
Baniso -1Baniso -2Baniso -3
1--12.63 Å20 Å22.58 Å2
2---0.12 Å20 Å2
3---12.94 Å2
Refinement stepCycle: LAST / Resolution: 3.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49350 0 0 0 49350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0470.02250595
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.3091.95568730
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18156225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.85824.4232340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.507158265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.97915240
X-RAY DIFFRACTIONr_chiral_restr0.20.27470
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0238880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2920.225544
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3510.233836
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.21719
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3740.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5961.532447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.476250490
X-RAY DIFFRACTIONr_scbond_it6.113321263
X-RAY DIFFRACTIONr_scangle_it8.2734.518240
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: 3290 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.165
loose thermal7.7510
LS refinement shellResolution: 3.3→3.381 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 508 -
Rwork0.344 9513 -
obs--92.51 %

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