[English] 日本語
Yorodumi
- PDB-3raa: Structural studies of AAV8 capsid transitions associated with end... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3raa
TitleStructural studies of AAV8 capsid transitions associated with endosomal trafficking
ComponentsCapsid proteinCapsid
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-5'-MONOPHOSPHATE / Capsid protein
Similarity search - Component
Biological speciesAdeno-associated virus - 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 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 1.1Jun 26, 2013Group: Database references
Revision 1.2Feb 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8762
Polymers58,5281
Non-polymers3471
Water0
1
A: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,532,535120
Polymers3,511,70260
Non-polymers20,83360
Water0
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
Water0
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
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)256.400, 256.400, 447.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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(0.56117, 0.75648, 0.3359), (-0.75842, 0.30744, 0.57469), (0.33148, -0.57725, 0.74626)74.7513, -18.8947, -56.9808
3generate(-0.15089, 0.46311, 0.87336), (-0.46922, -0.81116, 0.34906), (0.87009, -0.35713, 0.3397)83.3995, -113.9371, -63.7584
4generate(-0.14824, -0.47049, 0.86986), (0.4717, -0.80672, -0.35595), (0.86921, 0.35755, 0.34152)14.897, -153.60001, -10.723
5generate(0.56333, -0.75567, 0.33409), (0.75843, 0.31252, -0.57194), (0.32779, 0.57558, 0.74917)-36.83, -82.914, 28.7
6generate(0.64155, 0.7554, 0.1334), (0.17521, -0.31361, 0.93325), (0.74681, -0.57535, -0.33355)87.39, -224.56, 11.514
7generate(-0.17231, 0.64114, 0.74783), (0.64195, -0.50273, 0.57893), (0.74713, 0.57982, -0.32495)113.6182, -258.08511, 96.0509
8generate(-0.33866, -0.36553, 0.86701), (0.93203, -0.00407, 0.36235), (-0.12892, 0.93079, 0.34206)46.3016, -233.7032, 159.2587
9generate(0.37165, -0.86699, 0.33198), (0.64278, 0.49832, 0.58182), (-0.66986, -0.002839, 0.74248)-20.378, -184.32001, 113.59
10generate(0.97627, -0.17781, -0.12363), (0.17374, 0.30228, 0.93725), (-0.12928, -0.93649, 0.326)3.9892, -178.97, 22.221

-
Components

#1: Protein Capsid protein / Capsid


Mass: 58528.367 Da / Num. of mol.: 1 / Fragment: UNP residues 220-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 8 / Strain: Serotype 8 / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8JQF8
#2: Chemical ChemComp-A / ADENOSINE-5'-MONOPHOSPHATE / Adenosine monophosphate


Type: RNA linking / Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Tris pH 7.5, 4% PEG 4000, 1 M NaCl. Crystals were pre-soaked at pH 4 for 24 hours and transferred back to pH7.5 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 142296 / Num. obs: 126615 / % possible obs: 89 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.2→3.31 Å / % possible all: 88.2

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementResolution: 3.2→34.84 Å / Occupancy max: 1 / Occupancy min: 0.7 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2973 6311 4.4 %
Rwork0.2944 120304 -
obs-126615 89 %
Solvent computationBsol: -1.1325 Å2
Displacement parametersBiso max: 99.18 Å2 / Biso mean: 44.3399 Å2 / Biso min: 25.77 Å2
Baniso -1Baniso -2Baniso -3
1-10.394 Å20 Å20 Å2
2--10.394 Å20 Å2
3----20.787 Å2
Refinement stepCycle: LAST / Resolution: 3.2→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 18 0 4154
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0121.5
X-RAY DIFFRACTIONc_scbond_it1.2342
X-RAY DIFFRACTIONc_mcangle_it1.8192
X-RAY DIFFRACTIONc_scangle_it2.0562.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more