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- PDB-3shm: Structure-function Analysis of Receptor Binding in Adeno-Associat... -

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Basic information

Entry
Database: PDB / ID: 3shm
TitleStructure-function Analysis of Receptor Binding in Adeno-Associated Virus Serotype 6 (AAV-6)
ComponentsCapsid protein VP1
KeywordsVIRUS / beta barrel
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
Biological speciesAdeno-associated virus - 6
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.019 Å
AuthorsXie, Q. / Lerch, T.F. / Meyer, N.L. / Chapman, M.S.
CitationJournal: Virology / Year: 2011
Title: Structure-function analysis of receptor-binding in adeno-associated virus serotype 6 (AAV-6).
Authors: Xie, Q. / Lerch, T.F. / Meyer, N.L. / Chapman, M.S.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 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
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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)1,161,20620
Polymers1,161,20620
Non-polymers00
Water0
1
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1

A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1

A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)3,483,61960
Polymers3,483,61960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Buried area954200 Å2
ΔGint-4302 kcal/mol
Surface area835180 Å2
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1


  • crystal asymmetric unit, crystal frame
  • 1.16 MDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)1,161,20620
Polymers1,161,20620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
Unit cell
Length a, b, c (Å)258.357, 258.357, 612.966
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resid 221:736
211chain B and resid 221:736
311chain C and resid 221:736
411chain D and resid 221:736
511chain E and resid 221:736
611chain F and resid 221:736
711chain G and resid 221:736
811chain H and resid 221:736
911chain I and resid 221:736
1011chain J and resid 221:736
1111chain K and resid 221:736
1211chain L and resid 221:736
1311chain M and resid 221:736
1411chain N and resid 221:736
1511chain O and resid 221:736
1611chain P and resid 221:736
1711chain Q and resid 221:736
1811chain R and resid 221:736
1911chain S and resid 221:736
2011chain T and resid 221:736

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Components

#1: Protein
Capsid protein VP1 /


Mass: 58060.320 Da / Num. of mol.: 20 / Fragment: UNP residues 221-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 6 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: O56137

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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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.3
Details: 4-6% PEG6000, 100 mM HEPES, 50 mM magnesium, pH 7.3, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 3.019→48.672 Å / Num. all: 68828 / Num. obs: 68828 / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID
3.019-3.430.2751.151
3.43-4.330.1243.451
4.33-400.0726.771

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY AAV2

Resolution: 3.019→48.672 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.04 / σ(F): 0 / Phase error: 30.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2864 980 1.42 %
Rwork0.273 --
obs0.2732 68828 22.96 %
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.782 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--20.3609 Å20 Å20 Å2
2---20.3609 Å20 Å2
3---66.0176 Å2
Refine analyzeLuzzati coordinate error obs: 0.89 Å
Refinement stepCycle: LAST / Resolution: 3.019→48.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms82000 0 0 0 82000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284520
X-RAY DIFFRACTIONf_angle_d0.451115280
X-RAY DIFFRACTIONf_dihedral_angle_d10.74830320
X-RAY DIFFRACTIONf_chiral_restr0.03112040
X-RAY DIFFRACTIONf_plane_restr0.00315240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4100X-RAY DIFFRACTIONPOSITIONAL
12B4100X-RAY DIFFRACTIONPOSITIONAL0.006
13C4100X-RAY DIFFRACTIONPOSITIONAL0.007
14D4100X-RAY DIFFRACTIONPOSITIONAL0.006
15E4100X-RAY DIFFRACTIONPOSITIONAL0.006
16F4100X-RAY DIFFRACTIONPOSITIONAL0.007
17G4100X-RAY DIFFRACTIONPOSITIONAL0.006
18H4100X-RAY DIFFRACTIONPOSITIONAL0.007
19I4100X-RAY DIFFRACTIONPOSITIONAL0.007
110J4100X-RAY DIFFRACTIONPOSITIONAL0.007
111K4100X-RAY DIFFRACTIONPOSITIONAL0.006
112L4100X-RAY DIFFRACTIONPOSITIONAL0.006
113M4100X-RAY DIFFRACTIONPOSITIONAL0.007
114N4100X-RAY DIFFRACTIONPOSITIONAL0.007
115O4100X-RAY DIFFRACTIONPOSITIONAL0.007
116P4100X-RAY DIFFRACTIONPOSITIONAL0.006
117Q4100X-RAY DIFFRACTIONPOSITIONAL0.007
118R4100X-RAY DIFFRACTIONPOSITIONAL0.007
119S4100X-RAY DIFFRACTIONPOSITIONAL0.006
120T4100X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.019-3.177700.41367715X-RAY DIFFRACTION18
3.1777-3.37670.40372110.37815237X-RAY DIFFRACTION22
3.3767-3.63740.3022140.309410114X-RAY DIFFRACTION28
3.6374-4.00320.28292400.285613175X-RAY DIFFRACTION31
4.0032-4.58210.23161450.23889263X-RAY DIFFRACTION22
4.5821-5.77150.27091400.237912241X-RAY DIFFRACTION32
5.7715-48.67870.2432300.256810103X-RAY DIFFRACTION24

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