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- PDB-5w1o: Crystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosacc... -

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Basic information

Entry
Database: PDB / ID: 5w1o
TitleCrystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosaccharides
ComponentsMajor capsid protein L1
KeywordsVIRAL PROTEIN / human papillomavirus / jelly roll / capsid protein / receptor HSPG / virus capsid
Function / homology
Function and homology information


T=7 icosahedral viral capsid / symbiont entry into host cell / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDasgupta, J. / Chen, X.S.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Structural basis of oligosaccharide receptor recognition by human papillomavirus.
Authors: Dasgupta, J. / Bienkowska-Haba, M. / Ortega, M.E. / Patel, H.D. / Bodevin, S. / Spillmann, D. / Bishop, B. / Sapp, M. / Chen, X.S.
History
DepositionJun 4, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionOct 18, 2017ID: 3OAE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,21716
Polymers237,7485
Non-polymers6,46911
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40000 Å2
ΔGint-179 kcal/mol
Surface area81580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.620, 101.252, 128.182
Angle α, β, γ (deg.)90.00, 90.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Major capsid protein L1 / Late major capsid protein L1


Mass: 47549.547 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81007
#2: Polysaccharide
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 500.408 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ad122h-1a_1-5_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1465.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,6,5/[ad122h-1a_1-5_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG400, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.797→47.426 Å / Num. obs: 60092 / % possible obs: 98.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.28
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.353

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R5H

2r5h


Resolution: 2.8→47.43 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 3025 5.04 %
Rwork0.224 --
obs0.226 60060 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16687 0 390 147 17224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01617573
X-RAY DIFFRACTIONf_angle_d1.46923950
X-RAY DIFFRACTIONf_dihedral_angle_d17.6166320
X-RAY DIFFRACTIONf_chiral_restr0.0612634
X-RAY DIFFRACTIONf_plane_restr0.0063069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7971-2.84080.38571160.3142086X-RAY DIFFRACTION79
2.8408-2.88740.38751200.30222419X-RAY DIFFRACTION93
2.8874-2.93720.36841370.292516X-RAY DIFFRACTION96
2.9372-2.99060.36641260.28572609X-RAY DIFFRACTION98
2.9906-3.04810.30971510.27352581X-RAY DIFFRACTION99
3.0481-3.11030.3331370.27312629X-RAY DIFFRACTION99
3.1103-3.17790.30931330.2692619X-RAY DIFFRACTION100
3.1779-3.25180.33331240.26582640X-RAY DIFFRACTION100
3.2518-3.33310.36621620.26492619X-RAY DIFFRACTION100
3.3331-3.42320.31191270.23212606X-RAY DIFFRACTION100
3.4232-3.52390.2781370.22992635X-RAY DIFFRACTION100
3.5239-3.63760.29431440.23492636X-RAY DIFFRACTION100
3.6376-3.76760.26851430.21392631X-RAY DIFFRACTION100
3.7676-3.91840.25921390.21972625X-RAY DIFFRACTION100
3.9184-4.09660.26261440.21072641X-RAY DIFFRACTION100
4.0966-4.31240.21811440.18732628X-RAY DIFFRACTION100
4.3124-4.58240.21761270.18032673X-RAY DIFFRACTION100
4.5824-4.93590.19921210.16582630X-RAY DIFFRACTION100
4.9359-5.4320.21511430.17952654X-RAY DIFFRACTION100
5.432-6.21650.2861430.21832627X-RAY DIFFRACTION99
6.2165-7.82640.24511660.23062642X-RAY DIFFRACTION99
7.8264-47.43270.23871410.22562689X-RAY DIFFRACTION98
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)
12.3936-1.47461.35321.2078-0.69412.5312-0.0479-0.4882-0.72280.03630.28440.46660.3435-0.2431-0.21720.33830.01190.1020.22230.16010.374721.7623-32.833550.7836
21.4195-0.36760.10171.0450.15050.9211-0.1448-0.2933-0.1123-0.01050.24450.37070.2334-0.1598-0.06920.2687-0.04490.0760.2450.15550.376910.048-19.268849.9894
31.3776-0.9838-0.00931.042-0.45391.1014-0.0851-0.2928-0.19370.05560.20950.49050.1631-0.1518-0.08560.1923-0.01780.05260.27990.0710.44228.8827-14.823950.6544
42.3959-0.22661.92481.14970.33332.8691-0.0339-0.4393-0.66730.09920.37650.44940.47-0.2625-0.3380.40350.00560.12780.23550.16150.413218.9284-33.521650.7087
55.89982.1202-2.22815.9042-2.74974.46590.1664-0.14990.07550.0604-0.08460.2030.32130.08220.02280.25780.0657-0.02420.2328-0.03450.107439.9396-31.384746.0088
63.8982-0.35550.63232.0881-1.07571.5001-0.30190.4525-0.1482-0.54170.29650.43680.11510.4268-0.12540.4220.17260.17280.1936-0.2942-0.129938.162-22.296915.2585
71.9165-0.98810.27871.458-0.25730.66820.22610.0689-0.2129-0.4618-0.05940.27410.13580.0886-0.0350.4613-0.0273-0.08030.244-0.04040.16726.7092-20.471717.2817
84.20380.57880.1121.86830.25722.09390.12980.02-0.593-0.43260.14380.64060.5951-0.0674-0.05760.4695-0.0108-0.09610.17950.0070.395316.8025-33.829424.7513
90.6354-0.6105-0.15540.9229-0.10030.9198-0.07210.1639-0.2305-0.04390.06280.47050.2406-0.14290.01510.3257-0.075-0.09950.23860.02970.407311.6108-22.840528.2923
101.8191-3.57110.82928.3617-2.05020.4931-0.4478-0.27750.0920.59280.4409-0.13160.07120.1960.03180.30030.0369-0.01540.4573-0.05550.133541.0332-16.471927.199
111.447-0.27180.01241.01580.17330.26350.07720.25690.0735-0.3918-0.10320.20770.16020.18030.05180.4817-0.0323-0.02650.247-0.02380.181226.3181-13.57728.7706
127.95120.33561.2025.1849-0.16395.09330.19170.9165-0.5458-0.947-0.26290.69380.19450.40350.19160.69190.1835-0.16520.4483-0.2250.125450.2367-41.094320.5361
134.86951.3705-0.36744.94980.56552.17050.09360.4761-0.0976-0.0833-0.024-0.1370.46170.5411-0.05010.47130.11480.0550.3775-0.00470.109345.6033-18.332314.8469
145.10130.2821-0.09512.01210.72851.0546-0.2544-0.00440.4495-0.26410.0511-0.1646-0.15940.28260.17840.3809-0.11350.12440.25010.11640.039539.036516.925111.6044
155.61270.7845-1.11542.7044-0.56770.79390.1770.40650.457-0.187-0.0418-0.0144-0.37940.2963-0.09220.559-0.16210.00370.37940.01540.127536.455320.08846.6764
161.0724-0.17660.01871.7295-0.00011.01150.27480.0289-0.095-0.2195-0.12170.1185-0.04580.1-0.09080.363-0.004-0.02850.20480.08050.203525.31557.882213.5195
175.05261.29990.64852.5428-0.34120.1519-0.13720.5036-0.4182-0.77470.13820.3237-0.01970.3428-0.09130.5601-0.0644-0.11980.41410.06990.175726.2594-2.66810.2535
180.7282-0.1936-0.20531.272-0.06470.9723-0.04840.0564-0.1041-0.42910.09740.33040.1671-0.0402-0.02730.4263-0.0329-0.10660.24030.00550.270419.1433-4.91289.0268
191.5811-0.14740.04950.61230.12360.78050.16360.04470.1203-0.1997-0.06310.0895-0.11890.1418-0.10350.3681-0.0732-0.02630.2840.0540.181127.473815.816616.6563
202.27650.5706-1.2682.76881.97862.7119-0.06671.27620.4443-1.1558-0.3436-0.5962-0.50290.29980.31620.829-0.05860.29270.95550.18880.564258.040810.84340.1964
212.17360.87870.68142.58531.70486.40590.03130.26670.2644-0.18140.2644-0.4701-0.17510.5299-0.14230.4778-0.20130.16770.46790.05640.192944.292321.347716.5976
225.27851.19020.65271.1931-0.34063.2103-0.3634-0.72070.31310.21880.30150.1715-0.93760.1360.04460.3325-0.1133-0.03320.042-0.16090.25424.98732.955444.8472
231.98850.61140.3671.66480.78572.1243-0.0126-0.33120.3640.130.1733-0.1555-0.49390.4797-0.02410.3673-0.11680.02410.3018-0.12620.29923.860933.690644.8604
241.02870.17660.49741.11330.09772.0248-0.04720.06310.0803-0.25760.10030.2893-0.20380.0288-0.07240.2821-0.0011-0.05330.17990.0110.295613.987821.78422.708
257.38683.3869-0.91912.6175-0.6272.28750.18840.0879-0.01760.0074-0.1401-0.0534-0.45330.46130.03740.3381-0.0633-0.07670.2242-0.04650.292326.970127.743241.5658
262.82670.0563-0.29850.65310.39661.6693-0.2436-0.3990.5925-0.12620.27970.1896-0.73280.1972-0.04410.5531-0.07870.00340.187-0.02390.440520.239734.998144.0632
273.16560.34771.36093.38360.16425.5203-0.0078-0.44850.28980.0769-0.05830.0005-0.67570.47650.12840.1828-0.10650.04590.3871-0.10580.347929.428732.099552.161
280.64040.50471.21561.86120.28552.1465-0.32-0.3730.14060.03020.29920.80340.1540.0524-0.02460.14360.2070.27330.5172-0.08780.000512.9693.158770.584
290.05680.39070.22680.95830.47241.7587-0.13330.030.08230.01120.09550.25370.08040.0587-0.00920.16560.04070.10170.27550.06480.27058.46586.290954.573
30-0.0144-0.02820.16980.2676-0.0731.3084-0.0753-0.17940.06230.08960.19640.174-0.1906-0.1632-0.10340.20470.06050.03360.34790.03440.35547.577615.65752.1168
310.6121-0.3198-0.33250.49660.07361.5519-0.1684-0.2052-0.33210.40020.28810.59450.3559-0.62390.09810.2502-0.19280.13620.5890.34620.8147-8.1669-13.800351.4954
322.311.75220.94281.89010.92891.0117-0.1502-0.48140.27690.2268-0.06030.51730.0752-0.16860.23710.26130.12240.11890.5316-0.03940.352514.6437.708573.7231
334.2535-2.6502-2.0156.34561.53258.8644-0.2859-0.317-0.17630.1603-0.0684-0.07080.21220.86630.36230.27560.1943-0.03340.5259-0.0220.170429.1487-6.883171.7811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 20 THROUGH 86 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 87 THROUGH 181 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 182 THROUGH 344 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 345 THROUGH 450 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 451 THROUGH 474 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 20 THROUGH 56 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 57 THROUGH 160 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 161 THROUGH 209 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 210 THROUGH 301 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 302 THROUGH 324 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 325 THROUGH 382 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 383 THROUGH 439 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 440 THROUGH 474 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 20 THROUGH 56 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 57 THROUGH 86 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 87 THROUGH 160 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 161 THROUGH 209 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 210 THROUGH 290 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 291 THROUGH 382 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 383 THROUGH 439 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 440 THROUGH 474 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 20 THROUGH 56 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 57 THROUGH 125 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 126 THROUGH 312 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 313 THROUGH 344 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 345 THROUGH 439 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 440 THROUGH 473 )
28X-RAY DIFFRACTION28CHAIN 'E' AND (RESID 20 THROUGH 86 )
29X-RAY DIFFRACTION29CHAIN 'E' AND (RESID 87 THROUGH 160 )
30X-RAY DIFFRACTION30CHAIN 'E' AND (RESID 161 THROUGH 335 )
31X-RAY DIFFRACTION31CHAIN 'E' AND (RESID 336 THROUGH 356 )
32X-RAY DIFFRACTION32CHAIN 'E' AND (RESID 357 THROUGH 450 )
33X-RAY DIFFRACTION33CHAIN 'E' AND (RESID 451 THROUGH 473 )

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