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- PDB-3kic: Crystal structure of adeno-associated virus serotype 3B -

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Basic information

Entry
Database: PDB / ID: 3kic
TitleCrystal structure of adeno-associated virus serotype 3B
ComponentsCapsid protein VP1
KeywordsVIRUS / capsid / parvovirus / icosahedral virus / beta barrel / single-stranded / dependovirus
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
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Capsid protein VP1
Similarity search - Component
Biological speciesAdeno-associated virus 3B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.603 Å
AuthorsLerch, T.F. / Xie, Q. / Chapman, M.S.
Citation
Journal: Virology / Year: 2010
Title: The structure of adeno-associated virus serotype 3B (AAV-3B): insights into receptor binding and immune evasion.
Authors: Lerch, T.F. / Xie, Q. / Chapman, M.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Twinned crystals of adeno-associated virus serotype 3b prove suitable for structural studies
Authors: Lerch, T.F. / Xie, Q. / Ongley, H.M. / Hare, J. / Chapman, M.S.
History
DepositionNov 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Derived calculations / Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 31, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 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 / database_2 / pdbx_initial_refinement_model / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,646,36940
Polymers1,639,74420
Non-polymers6,62420
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
hetero molecules

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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,939,106120
Polymers4,919,23360
Non-polymers19,87360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
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
hetero molecules


  • crystal asymmetric unit, crystal frame
  • 1.65 MDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)1,646,36940
Polymers1,639,74420
Non-polymers6,62420
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
Unit cell
Length a, b, c (Å)257.704, 257.704, 603.766
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and resid 217:737A217 - 737
211chain B and resid 217:737B217 - 737
311chain C and resid 217:737C217 - 737
411chain D and resid 217:737D217 - 737
511chain E and resid 217:737E217 - 737
611chain F and resid 217:737F217 - 737
711chain G and resid 217:737G217 - 737
811chain H and resid 217:737H217 - 737
911chain I and resid 217:737I217 - 737
1011chain J and resid 217:737J217 - 737
1111chain K and resid 217:737K217 - 737
1211chain L and resid 217:737L217 - 737
1311chain M and resid 217:737M217 - 737
1411chain N and resid 217:737N217 - 737
1511chain O and resid 217:737O217 - 737
1611chain P and resid 217:737P217 - 737
1711chain Q and resid 217:737Q217 - 737
1811chain R and resid 217:737R217 - 737
1911chain S and resid 217:737S217 - 737
2011chain T and resid 217:737T217 - 737

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Components

#1: Protein
Capsid protein VP1 /


Mass: 81987.219 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 3B / Gene: Cap / Plasmid: pAAV3B / Cell line (production host): HeLa / Production host: Homo sapiens (human) / References: UniProt: O56139
#2: Chemical
ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Mass: 331.222 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C10H14N5O6P

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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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.3
Details: 3.2-3.4% PEG 6000, 50mM magnesium chloride, 100mM hepes, 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 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2004
RadiationMonochromator: 0.916 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.475
ReflectionResolution: 2.6→100 Å / Num. all: 177514 / Num. obs: 147388 / % possible obs: 32.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.2 % / Rmerge(I) obs: 0.066 / Χ2: 0.85 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allDiffraction-ID% possible allRmerge(I) obsΧ2
2.6-2.6613727112.2
2.66-2.7314412114.4
2.73-2.815429117.80.5321.827
2.8-2.8816768122.10.4221.732
2.88-2.981.18209126.90.3011.506
2.98-3.081.110240133.60.2111.073
3.08-3.211.110796135.20.1591.098
3.21-3.351.210985135.90.1281.096
3.35-3.531.211521137.60.1051.012
3.53-3.751.212081139.60.0890.855
3.75-4.041.312463140.70.080.783
4.04-4.451.312995142.50.0670.583
4.45-5.091.413400143.80.0580.773
5.09-6.411.413276143.30.0550.798
6.41-1001.211086136.30.0470.83

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lp3

1lp3


Resolution: 2.603→14.99 Å / Occupancy max: 1 / Occupancy min: 0.7 / σ(F): 1.96 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.218 5095 3.99 %thin resolution shells
Rwork0.19 ---
obs0.19 127791 28.05 %-
all-127791 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.056 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 163.39 Å2 / Biso mean: 90.642 Å2 / Biso min: 51.3 Å2
Baniso -1Baniso -2Baniso -3
1--26.838 Å20 Å20 Å2
2---26.838 Å20 Å2
3---28.936 Å2
Refinement stepCycle: LAST / Resolution: 2.603→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms83080 0 440 0 83520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00386120
X-RAY DIFFRACTIONf_angle_d0.746117620
X-RAY DIFFRACTIONf_chiral_restr0.04712200
X-RAY DIFFRACTIONf_plane_restr0.00315600
X-RAY DIFFRACTIONf_dihedral_angle_d16.44830480
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4176X-RAY DIFFRACTIONPOSITIONAL0.001
12B4176X-RAY DIFFRACTIONPOSITIONAL0.001
13C4176X-RAY DIFFRACTIONPOSITIONAL0.001
14D4176X-RAY DIFFRACTIONPOSITIONAL0.002
15E4176X-RAY DIFFRACTIONPOSITIONAL0.001
16F4176X-RAY DIFFRACTIONPOSITIONAL0.001
17G4176X-RAY DIFFRACTIONPOSITIONAL0.001
18H4176X-RAY DIFFRACTIONPOSITIONAL0.001
19I4176X-RAY DIFFRACTIONPOSITIONAL0.001
110J4176X-RAY DIFFRACTIONPOSITIONAL0.001
111K4176X-RAY DIFFRACTIONPOSITIONAL0.001
112L4176X-RAY DIFFRACTIONPOSITIONAL0.002
113M4176X-RAY DIFFRACTIONPOSITIONAL0.001
114N4176X-RAY DIFFRACTIONPOSITIONAL0.002
115O4176X-RAY DIFFRACTIONPOSITIONAL0.001
116P4176X-RAY DIFFRACTIONPOSITIONAL0.001
117Q4176X-RAY DIFFRACTIONPOSITIONAL0.002
118R4176X-RAY DIFFRACTIONPOSITIONAL0.001
119S4176X-RAY DIFFRACTIONPOSITIONAL0.001
120T4176X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.603-2.6480.3772571
2.648-2.6960.3543039
2.696-2.7480.3433453
2.748-2.8030.3583790.34614681847
2.803-2.8640.3423448
2.864-2.930.345639
2.93-3.0030.315560.31859756531
3.003-3.0830.3127742
3.083-3.1730.3046789
3.173-3.2740.2956130.27441184731
3.274-3.390.2568133
3.39-3.5240.2125310.22881898720
3.524-3.6820.2138995
3.682-3.8730.1954939
3.873-4.1110.2054840.17289519435
4.111-4.4210.159770
4.421-4.8520.1774150.14364766891
4.852-5.5240.1692230.149994410167
5.524-6.8470.136240.15278177841
6.847-14.990.186930.13270177110

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