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- PDB-5j6r: Crystal structure of Human Papillomavirus Type 59 L1 pentamer -

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Basic information

Entry
Database: PDB / ID: 5j6r
TitleCrystal structure of Human Papillomavirus Type 59 L1 pentamer
ComponentsMajor capsid protein L1
KeywordsVIRAL PROTEIN / Major structural protein / Pentamer
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) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus type 59
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.011 Å
AuthorsLi, Z.H. / Yan, X.D. / Yu, H. / Gu, Y. / Li, S.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation81172885 China
CitationJournal: Structure / Year: 2016
Title: The C-Terminal Arm of the Human Papillomavirus Major Capsid Protein Is Immunogenic and Involved in Virus-Host Interaction.
Authors: Zhihai Li / Xiaodong Yan / Hai Yu / Daning Wang / Shuo Song / Yunbing Li / Maozhou He / Qiyang Hong / Qingbing Zheng / Qinjian Zhao / Ying Gu / Jun Zhang / Mandy E W Janssen / Giovanni ...Authors: Zhihai Li / Xiaodong Yan / Hai Yu / Daning Wang / Shuo Song / Yunbing Li / Maozhou He / Qiyang Hong / Qingbing Zheng / Qinjian Zhao / Ying Gu / Jun Zhang / Mandy E W Janssen / Giovanni Cardone / Norman H Olson / Timothy S Baker / Shaowei Li / Ningshao Xia /
Abstract: Cervical cancer is the second most prevalent malignant tumor among women worldwide. High-risk human papillomaviruses (HPVs) are believed to be the major causative pathogens of mucosal epithelial ...Cervical cancer is the second most prevalent malignant tumor among women worldwide. High-risk human papillomaviruses (HPVs) are believed to be the major causative pathogens of mucosal epithelial cancers including cervical cancer. The HPV capsid is made up of 360 copies of major (L1) and 72 copies of minor (L2) capsid proteins. To date, limited high-resolution structural information about the HPV capsid has hindered attempts to understand details concerning the mechanisms by which HPV assembles and infects cells. In this study, we have constructed a pseudo-atomic model of the HPV59 L1-only capsid and demonstrate that the C-terminal arm of L1 participates in virus-host interactions. Moreover, when conjugated to a scaffold protein, keyhole limpet hemocyanin (KLH), this arm is immunogenic in vivo. These results provide new insights that will help elucidate HPV biology, and hence pave a way for the design of next-generation HPV vaccines.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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


Theoretical massNumber of molelcules
Total (without water)559,62410
Polymers559,62410
Non-polymers00
Water0
1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
H: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)279,8125
Polymers279,8125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36720 Å2
ΔGint-162 kcal/mol
Surface area77390 Å2
MethodPISA
2
E: Major capsid protein L1
F: Major capsid protein L1
G: Major capsid protein L1
I: Major capsid protein L1
J: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)279,8125
Polymers279,8125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37250 Å2
ΔGint-160 kcal/mol
Surface area77700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.242, 161.743, 154.729
Angle α, β, γ (deg.)90.00, 110.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 17:401 or resseq 436:470 )
211chain 'B' and (resseq 17:171 or resseq 176:401 or resseq 436:470 )
311chain 'C' and (resseq 17:401 or resseq 436:470 )
411chain 'D' and (resseq 17:401 or resseq 436:470 )
511chain 'E' and (resseq 17:401 or resseq 436:470 )
611chain 'F' and (resseq 17:401 or resseq 436:470 )
711chain 'G' and (resseq 17:401 or resseq 436:470 )
811chain 'H' and (resseq 17:169 or resseq 176:401 or resseq 436:470 )
911chain 'I' and (resseq 17:401 or resseq 436:470 )
1011chain 'J' and (resseq 17:401 or resseq 436:470 )

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Components

#1: Protein
Major capsid protein L1


Mass: 55962.355 Da / Num. of mol.: 10 / Fragment: UNP RESIDUES 10-508 / Mutation: C175S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 59 / Gene: ORF putative L1, L1 / Plasmid: pTO-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q81971

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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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 44094 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 85.6 Å2 / Rsym value: 0.283 / Net I/σ(I): 7.8
Reflection shellResolution: 4→4.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.854 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R5I

2r5i


Resolution: 4.011→49.697 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.2671 2232 5.07 %
Rwork0.2428 --
obs0.244 44025 99.37 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 71.912 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1382 Å2-0 Å2-1.346 Å2
2--43.2817 Å20 Å2
3----44.4199 Å2
Refinement stepCycle: LAST / Resolution: 4.011→49.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33270 0 0 0 33270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434136
X-RAY DIFFRACTIONf_angle_d0.69546455
X-RAY DIFFRACTIONf_dihedral_angle_d12.92712459
X-RAY DIFFRACTIONf_chiral_restr0.0455087
X-RAY DIFFRACTIONf_plane_restr0.0036026
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3305X-RAY DIFFRACTIONPOSITIONAL
12B3305X-RAY DIFFRACTIONPOSITIONAL0.035
13C3334X-RAY DIFFRACTIONPOSITIONAL0.023
14D3334X-RAY DIFFRACTIONPOSITIONAL0.03
15E3334X-RAY DIFFRACTIONPOSITIONAL0.021
16F3334X-RAY DIFFRACTIONPOSITIONAL0.013
17G3334X-RAY DIFFRACTIONPOSITIONAL0.007
18H3293X-RAY DIFFRACTIONPOSITIONAL0.008
19I3334X-RAY DIFFRACTIONPOSITIONAL0.026
110J3334X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0114-4.09850.30381230.30952437X-RAY DIFFRACTION92
4.0985-4.19380.32871500.29912578X-RAY DIFFRACTION100
4.1938-4.29870.32181360.29142645X-RAY DIFFRACTION100
4.2987-4.41480.29941420.26912598X-RAY DIFFRACTION100
4.4148-4.54460.29541380.24982615X-RAY DIFFRACTION100
4.5446-4.69120.26541350.23512608X-RAY DIFFRACTION100
4.6912-4.85870.29341380.22392619X-RAY DIFFRACTION100
4.8587-5.05310.26261450.21282630X-RAY DIFFRACTION100
5.0531-5.28280.27981490.23362607X-RAY DIFFRACTION100
5.2828-5.5610.20361590.22362591X-RAY DIFFRACTION100
5.561-5.90890.28141630.24452594X-RAY DIFFRACTION100
5.9089-6.36430.26561320.24332670X-RAY DIFFRACTION100
6.3643-7.00320.22421210.22042628X-RAY DIFFRACTION100
7.0032-8.01290.21951560.2062620X-RAY DIFFRACTION100
8.0129-10.08150.20811110.18512687X-RAY DIFFRACTION100
10.0815-49.70060.2841340.28372666X-RAY DIFFRACTION99
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)
11.35590.4191-0.16220.4833-0.29841.4086-0.02330.30660.1985-0.28610.20460.1099-0.2489-0.0449-0.1770.64580.01590.00680.27240.02150.4433-18.105814.254665.7137
20.9618-0.02-0.05090.62510.19521.5633-0.01540.22680.3878-0.0678-0.0067-0.2178-0.24740.3627-0.03190.4392-0.18550.07020.2183-0.08290.49229.427325.487678.4743
30.85580.3627-0.35560.7648-0.4392.0721-0.01110.3617-0.2436-0.37310.1179-0.16190.06380.0797-0.08060.56910.0179-0.02830.4255-0.20420.4691-16.3169-18.2864.6856
40.62350.07820.1360.2292-0.03691.94660.02860.2444-0.2364-0.26550.0563-0.4244-0.04770.3638-0.07150.47360.05420.20150.6525-0.18570.571328.7144-0.190185.4258
51.30560.3112-0.25830.8409-0.05971.76920.0658-0.6037-0.11360.342-0.06980.0121-0.0013-0.39720.04730.5406-0.044-0.1680.67910.11930.3121-1.3207-6.5864153.9504
61.02050.4888-0.40010.4986-0.20461.69690.0603-0.74520.03650.262-0.0680.22720.0267-0.53490.13540.55380.2129-0.04950.6546-0.5930.164-18.122120.7844148.2196
70.89280.23370.06320.4648-0.08921.77080.0714-0.6791-0.2230.2866-0.07440.2350.3634-0.57310.00470.4516-0.19410.03380.84850.07540.5163-47.8101-20.0933133.0963
80.485-0.04720.17520.95360.19311.8964-0.00580.4038-0.4293-0.1540.1065-0.33710.26870.4381-0.12310.64580.07150.10680.6718-0.28880.921312.799-26.989877.1765
90.60930.07370.06340.2530.06230.95760.2627-0.6757-0.20830.2423-0.15550.09430.29-0.1837-0.02560.4307-0.1357-0.24790.50520.5550.1924-19.6885-31.8748144.5553
100.62230.11810.1740.7145-0.05371.56340.0948-0.63660.18890.2695-0.25740.4253-0.0294-0.53390.12950.47230.27040.09551.0691-0.36380.6918-46.829812.4618135.3298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'
7X-RAY DIFFRACTION7chain 'G'
8X-RAY DIFFRACTION8chain 'H'
9X-RAY DIFFRACTION9chain 'I'
10X-RAY DIFFRACTION10chain 'J'

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