[English] 日本語
Yorodumi
- PDB-3ra4: Structural studies of AAV8 capsid transitions associated with end... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ra4
TitleStructural studies of AAV8 capsid transitions associated with endosomal trafficking
Components
  • Capsid protein
  • DNA (5'-D(*CP*A)-3')
KeywordsVIRUS / beta barrel / Viral Capsid / Receptor
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
DNA / Capsid protein
Similarity search - Component
Biological speciesAdeno-associated virus - 8
Aequorea victoria (jellyfish)
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 1.1Jun 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
D: DNA (5'-D(*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)59,0862
Polymers59,0862
Non-polymers00
Water1,36976
1
A: Capsid protein
D: DNA (5'-D(*CP*A)-3')
x 60


Theoretical massNumber of molelcules
Total (without water)3,545,148120
Polymers3,545,148120
Non-polymers00
Water2,162120
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
D: DNA (5'-D(*CP*A)-3')
x 5


  • icosahedral pentamer
  • 295 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)295,42910
Polymers295,42910
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
D: DNA (5'-D(*CP*A)-3')
x 6


  • icosahedral 23 hexamer
  • 355 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)354,51512
Polymers354,51512
Non-polymers00
Water21612
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
D: DNA (5'-D(*CP*A)-3')
x 10


  • crystal asymmetric unit, crystal frame
  • 591 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)590,85820
Polymers590,85820
Non-polymers00
Water36020
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.)90.00, 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(0.56326, 0.75471, 0.33637), (-0.75707, 0.3083, 0.57602), (0.33103, -0.57911, 0.74502)74.9414, -18.6809, -57.3758
3generate(-0.14435, 0.4643, 0.87384), (-0.46857, -0.80988, 0.35291), (0.87155, -0.35851, 0.33446)83.9955, -114.3114, -64.4232
4generate(-0.14511, -0.4705, 0.87039), (0.4686, -0.80746, -0.35836), (0.87141, 0.35586, 0.33765)14.614, -154.8, -11.322
5generate(0.56249, -0.75744, 0.33149), (0.75701, 0.31058, -0.57488), (0.33248, 0.57431, 0.74808)-37.403, -84.161, 28.243
6generate(0.64299, 0.75461, 0.13087), (0.17675, -0.31247, 0.93334), (0.7452, -0.577, -0.33429)87.77, -225.53999, 10.528
7generate(-0.16789, 0.643088, 0.74717), (0.64317, -0.50294, 0.57739), (0.74709, 0.5775, -0.32918)114.6243, -259.84171, 96.1499
8generate(-0.33486, -0.36095, 0.87039), (0.93375, -0.00317, 0.35792), (-0.12644, 0.93258, 0.3381)47.2147, -235.30589, 160.2977
9generate(0.3715, -0.86776, 0.33012), (0.64501, 0.49698, 0.58049), (-0.66779, -0.00272, 0.74435)-20.967, -185.67999, 114.37
10generate(0.97566, -0.17934, -0.12616), (0.17713, 0.30545, 0.93559), (-0.12925, -0.93517, 0.32979)3.9687, -179.63, 21.814

-
Components

#1: Protein Capsid protein


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: DNA chain DNA (5'-D(*CP*A)-3')


Mass: 557.431 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE VIRUS CAPSID IS FROM AAV8 VIRUS BUT THE GENE ENCAPSULATED BY THE VIRUS WAS GFP. ONLY TWO ...THE VIRUS CAPSID IS FROM AAV8 VIRUS BUT THE GENE ENCAPSULATED BY THE VIRUS WAS GFP. ONLY TWO 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: 3

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Tris pH7.5, 4% PEG 8000, 1M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2007
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: 238726 / Num. obs: 221840 / % possible obs: 92.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rsym value: 0.083
Reflection shellResolution: 2.7→2.8 Å / Rsym value: 0.201 / % possible all: 58.3

-
Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.213 10909 RANDOM
Rwork0.212 --
obs0.212 221840 -
all-238726 -
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 37 0 76 4249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6

+
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