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Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20
by single particle (icosahedral) reconstruction, at 8.5 A resolution
#1: Biological unit as complete icosahedral assembly, Made by Jmol
#2: Biological unit as icosahedral pentamer, Made by Jmol
#3: Biological unit as icosahedral 23 hexamer, Made by Jmol
#4: Depositted structure unit, Made by Jmol
#5: Superimposing with simplified surface model of EM map, EMDB-5424, Made by Jmol
#6: Superimposing with EM 3D map: EMDB-5424, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3j1s |
|---|---|
| Title | Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20 |
| Descriptor | A20 light chain A20 heavy chain Capsid protein VP1 |
| Keywords |  VIRUS/IMMUNE SYSTEM, Epitope, Fab, gene therapy, VIRUS-IMMUNE SYSTEM complex |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Sequence details | DUE TO IN-FRAME ALTERNATIVE SPLICING, THE AAV-2 CAPSID PROTEIN IN THIS ENTRY IS A 1:1:10 MIXTURE OF ISOFORMS VP1, VP2, AND VP3. THE SEQUENCE MODELED (UNP RESIDUES 217-735) IS COMMON TO ALL THREE ISOFORMS. THE VARIABLE DOMAINS OF FAB' A20 (RESIDUES 1-107 OF THE LIGHT CHAIN AND RESIDUES 1-120 OF THE HEAVY CHAIN) ARE A HOMOLOGY MODEL DERIVED FROM SEQUENCING INFORMATION. THE CONSERVED CONSTANT DOMAINS (RESIDUES 108-214 OF THE LIGHT CHAIN AND RESIDUES 121-218 OF THE HEAVY CHAIN) ARE FROM PDB ENTRY 1OSP AND ARE AN APPROXIMATION OF THE ACTUAL SEQUENCE OF FAB' A20. |
| Structure Visualization | |
| Movies |  Movie Page#1: Biological unit as complete icosahedral assembly, Made by Jmol #2: Biological unit as icosahedral pentamer, Made by Jmol #3: Biological unit as icosahedral 23 hexamer, Made by Jmol #4: Depositted structure unit, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-5424, Made by Jmol #6: Superimposing with EM 3D map: EMDB-5424, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | Virology, Vol. 431, Page: 40 - 49, Year: 2012, |
|---|---|
| Title | Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20. |
| Authors | McCraw, D.M., O'Donnell, J.K., Taylor, K.A., Stagg, S.M., Chapman, M.S. |
| Links | DOI: 10.1016/j.virol.2012.05.004 |
 Components | |
| ID 1 : A20 light chain | |
| Image |   |
|---|---|
| Description | A20 light chain |
| Type | polypeptide(L) |
| Fragment | Fab' |
| Formula weight | 23604.145 Da |
| Number of molecules | 1 |
| ID | 1 |
| Source | Method: Isolated from a natural source Common name: mouse NCBI taxonomy: ID:10090Organism scientific: Mus musculus
|
| Links | Sequence view |
| ID 2 : A20 heavy chain | |
| Image |   |
| Description | A20 heavy chain |
| Type | polypeptide(L) |
| Fragment | Fab' |
| Formula weight | 23777.459 Da |
| Number of molecules | 1 |
| ID | 2 |
| Source | Method: Isolated from a natural source Common name: mouse NCBI taxonomy: ID:10090Organism scientific: Mus musculus |
| Links | Sequence view |
| ID 3 : Coat protein VP1 | |
| Image |   |
| Description | Capsid protein VP1 |
| Type | polypeptide(L) |
| Fragment | SEE REMARK 999 |
| Formula weight | 58773.250 Da |
| Number of molecules | 1 |
| ID | 3 |
| Source | Method: Isolated from a natural source Common name: AAV-2 NCBI taxonomy: ID:10804Organism scientific: Adeno-associated virus - 2 |
| Links | UniProt: P03135, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Composition | 60 A20 Fab's bind to one adeno-associated virus (one adeno-associated virus consists of 60 viral proteins) |
| Details | Infectious DNA-containing particle (DNA not resolved) |
| Theoretical Mass | 6.9 |
| Name | Adeno-associated virus-2 in complex with monoclonal antibody A20 |
| Num components | 2 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | Fab' fragment generated by pepsin cleavage of A20 IgG antibody. |
| GO-ID | GO:0071735 |
| InterPro-ID | IPR:013783 |
| Name | Antibody Fab' fragment |
| Type | VIRUS |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | Fab' fragment generated by pepsin cleavage of A20 IgG antibody. |
| GO-ID | GO:0071735 |
| InterPro-ID | IPR:013783 |
| Name | Antibody Fab' Fragment |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | Viral capsid protein monomer for AAV-2 |
| GO-ID | GO:0019069 |
| InterPro-ID | IPR:001403 |
| Name | Viral protein |
| Virus entity | |
| Virus host category | VERTEBRATES |
| Virus host species | Homo sapiens |
| Virus isolate | SEROTYPE |
| Virus type | VIRION |
| Virus entity | |
| Ictvdb id | 10804 |
| Virus host category | Vertebrates |
| Virus host growth cell | HeLa |
| Virus host species | Homo Sapiens |
| Virus isolate | SEROTYPE |
| Virus type | Single-stranded DNA Parvovirus |
| Buffer | |
| Name | 100 mM HEPES, 50 mM magnesium chloride, 5% glycerol |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| Details | 100 mM HEPES, 50 mM magnesium chloride, 5% glycerol |
| pH | 7.2 |
| Sample concentration | 0.14 mg/ml |
| Sample support | |
| Details | 400 mesh carbon grid with holey carbon support |
| Vitrification | |
| Cryogen name | ETHANE |
| Details | Blot for 2.0 seconds before plunging into liquid ethane (FEI Vitrobot Mark IV). |
| Humidity | 100 |
| Instrument | FEI Vitrobot Mark IV |
| Method | Blot for 2.0 seconds before plunging. |
| Temp | 90 Kelvin |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 Electron Microscopy | |
| Imaging | |
| Microscope | Model: FEI Titan Krios |
|---|---|
| Date | 2011-02-23 |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 120 kV |
| Electron dose | 15 e/A**2 |
| Illumination mode | SPOTSCAN |
| Lens | |
| Mode | BRIGHTFIELD |
| Magnification | Calibrated: 39775 X, Nominal: 37000 X |
| Cs | Nominal: 2.7 mm |
| Astigmatism | Objective lens astigmatism was corrected at 120,000 times magnification |
| Detector distance | 0.0 |
| Nominal defocus | Max: -4000 nm, Min: -500 nm |
| Specimen holder | |
| Specimen holder | Model: OTHER, Type: Nitrogen cooled |
| Tilt angle | Min: 0.0 degrees, Max: 0.0 degrees |
| Temperature | 93 Kelvin |
| Detector | |
| Type | Gatan Ultrascan CCD |
| Image scans | |
| Number digital images | 1503 |
 Processing | |
| 2D projection selection | |
| Number of particles | 11898 |
|---|---|
| Software name | RSRef |
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
| 3D reconstruction | |
| Actual pixel size | 2.45 A/pix |
| CTF correction method | Whole image |
| Details | A20 FAB' WAS MODELED AS THE COMBINATION OF A HOMOLOGY MODEL AND SEQUENCE SEGMENTS EXCERPTED FROM PDB ENTRY 1OSP (SEE REMARK 999 FOR DETAILS). THE AUTHORS STATE THAT ANY INCORRECT PEPTIDE BOND LENGTHS IN THIS ENTRY ARE THE RESULT OF RIGID-BODY FITTING TO A LOW-RESOLUTION MAP OR ARE INHERITED DIRECTLY FROM PDB ENTRY 1OSP. |
| Method | Common-lines |
| Nominal pixel size | 2.45 A/pix |
| Num class averages | 304 |
| Number of particles | 11898 |
| Resolution | 8.5 A |
| Resolution method | FSC at 0.5 cut-off |
| Software | Appion, ACE, EMAN |
| 3D fitting | |
| Details | Anti-bumping restraints from CNS, Constrained icosahedral symmetry |
| Method | Rigid Body |
| Temperature factor | 0.0 |
| Refinement Protocol | Rigid Body |
| Refinement Space | REAL |
| Software name | RSRef |
| Target criteria | Least-squares difference between experimental & model coulombic potential |
| 3D fitting | |
| Details | Anti-bumping restraints from CNS, Constrained icosahedral symmetry |
| Method | Rigid Body |
| Temperature factor | 0.0 |
| Refinement Protocol | Rigid Body |
| Refinement Space | REAL |
| Software name | RSRef |
| Target criteria | Least-squares difference between experimental & model coulombic potential |
| 3D fitting | |
| Details | Anti-bumping restraints from CNS included 1LP3, Constrained icosahedral symmetry |
| Method | Superimposed according to icosahedral symmetry |
| Temperature factor | 0.0 |
| Refinement Protocol | Fixed |
| Refinement Space | REAL |
| Software name | RSRef |
| Target criteria | Least-squares difference between experimental & model coulombic potential |
| 3D fitting list | |
| 3D fitting id | 1 |
| Pdb chain id | A |
| PDB entry ID | 1LP3 |
| Refine | |
| Refine id | ELECTRON MICROSCOPY |
| Details | A20 FAB' WAS MODELED AS THE COMBINATION OF A HOMOLOGY MODEL AND SEQUENCE SEGMENTS EXCERPTED FROM PDB ENTRY 1OSP (SEE REMARK 999 FOR DETAILS). THE AUTHORS STATE THAT ANY INCORRECT PEPTIDE BOND LENGTHS IN THIS ENTRY ARE THE RESULT OF RIGID-BODY FITTING TO A LOW-RESOLUTION MAP OR ARE INHERITED DIRECTLY FROM PDB ENTRY 1OSP. |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| Total atoms | 7485 |
| Protein atoms | 7485 |
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