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- PDB-3ra8: Structural studies of AAV8 capsid transitions associated with end... -

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Basic information

Entry
Database: PDB / ID: 3ra8
TitleStructural studies of AAV8 capsid transitions associated with endosomal trafficking
ComponentsCapsid protein
KeywordsVIRUS / Beta Barrel / Viral Capsid
Function / homology
Function and homology information


T=1 icosahedral viral capsid / structural molecule activity
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Capsid protein
Similarity search - Component
Biological speciesAdeno-associated virus - 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNam, H.-J. / Gurda, B. / McKenna, R. / Porter, M. / Byrne, B. / Salganik, M. / Muzyczka, N. / Agbandje-McKenna, M.
CitationJournal: J.Virol. / Year: 2011
Title: Structural studies of adeno-associated virus serotype 8 capsid transitions associated with endosomal trafficking.
Authors: Nam, H.J. / Gurda, B.L. / McKenna, R. / Potter, M. / Byrne, B. / Salganik, M. / Muzyczka, N. / Agbandje-McKenna, M.
History
DepositionMar 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Other
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Feb 21, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8762
Polymers58,5281
Non-polymers3471
Water1,53185
1
A: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,532,535120
Polymers3,511,70260
Non-polymers20,83360
Water1,08160
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: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 294 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)294,37810
Polymers292,6425
Non-polymers1,7365
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 353 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)353,25412
Polymers351,1706
Non-polymers2,0836
Water1086
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: Capsid protein
hetero molecules
x 10


  • crystal asymmetric unit, crystal frame
  • 589 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)588,75620
Polymers585,28410
Non-polymers3,47210
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)257.940, 257.940, 448.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.56344, 0.7547, 0.3361), (-0.75606, 0.30704, 0.57802), (0.33304, -0.57979, 0.74359)74.8651, -18.8343, -57.549
3generate(-0.14137, 0.46317, 0.87492), (-0.46843, -0.80989, 0.35306), (0.87212, -0.35993, 0.33146)83.5237, -114.0967, -64.5545
4generate(-0.147, -0.47088, 0.86986), (0.46704, -0.80825, -0.35861), (0.87193, 0.35355, 0.33874)15.196, -154.61, -11.77
5generate(0.56101, -0.7589, 0.33065), (0.75735, 0.30928, -0.57513), (0.3342, 0.57307, 0.74826)-36.959, -84.267, 27.764
6generate(0.64282, 0.75508, 0.12897), (0.17954, -0.31219, 0.9329), (0.74468, -0.57653, -0.33625)87.978, -225.66, 10.951
7generate(-0.16771, 0.64189, 0.74823), (0.64367, -0.50358, 0.57628), (0.7467, 0.57826, -0.32871)114.4044, -259.40659, 95.9389
8generate(-0.33352, -0.36195, 0.87049), (0.93424, -0.00318, 0.35663), (-0.12631, 0.93219, 0.33921)47.0251, -234.9754, 159.9884
9generate(0.37021, -0.86841, 0.32986), (0.64592, 0.49584, 0.58045), (-0.66763, -0.001828, 0.74449)-20.641, -185.92999, 114.34
10generate(0.97576, -0.17803, -0.12725), (0.17751, 0.30385, 0.93604), (-0.12798, -0.93594, 0.32809)4.2744, -179.83, 21.976

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Components

#1: Protein Capsid protein


Mass: 58528.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 8 / Strain: Serotype 8 / Gene: Adeno Associated Virus / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8JQF8
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE VIRUS CAPSID IS FROM AAV8 VIRUS BUT THE GENE ENCAPSULATED BY THE VIRUS WAS GFP. ONLY ONE ...THE VIRUS CAPSID IS FROM AAV8 VIRUS BUT THE GENE ENCAPSULATED BY THE VIRUS WAS GFP. ONLY ONE RESIDUE WAS OBSERVED IN THE ELECTRON DENSITY MAP FROM THE GENE CODING GFP IN THIS STRUCTURE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 mM Tris pH 7.5, 4% PEG 8000, 1M NaCl. Crystals presoaked in pH 5.5 cryosolvent for 24 hours before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 238727 / Num. obs: 185894 / % possible obs: 77.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.7→2.8 Å / % possible all: 57.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40 Å / Occupancy max: 1 / Occupancy min: 0.7 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 9148 3.8 %RANDOM
Rwork0.2454 ---
obs0.246 185894 77.9 %-
all-238727 --
Solvent computationBsol: 30.3674 Å2
Displacement parametersBiso max: 103.14 Å2 / Biso mean: 38.1277 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1-7.867 Å2-0 Å20 Å2
2--7.867 Å20 Å2
3----15.735 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 23 85 4244
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0351.5
X-RAY DIFFRACTIONc_scbond_it1.6942
X-RAY DIFFRACTIONc_mcangle_it1.8252
X-RAY DIFFRACTIONc_scangle_it2.6762.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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