[English] 日本語
Yorodumi
- PDB-1qiu: A triple beta-spiral in the adenovirus fibre shaft reveals a new ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qiu
TitleA triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for biological fibres
ComponentsADENOVIRUS FIBRE
KeywordsFIBRE PROTEIN / TRIPLE BETA-SPIRAL / ADENOVIRUS
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
reovirus attachment protein sigma1; domain 1 / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain ...reovirus attachment protein sigma1; domain 1 / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Laminin / Ribbon / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHUMAN ADENOVIRUS 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Authorsvan Raaij, M.J. / Lavigne, G. / Mitraki, A. / Cusack, S.
CitationJournal: Nature / Year: 1999
Title: A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein.
Authors: van Raaij, M.J. / Mitraki, A. / Lavigne, G. / Cusack, S.
History
DepositionJun 16, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Feb 7, 2024Group: Structure summary / Category: entity / Item: _entity.pdbx_fragment

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADENOVIRUS FIBRE
B: ADENOVIRUS FIBRE
C: ADENOVIRUS FIBRE
D: ADENOVIRUS FIBRE
E: ADENOVIRUS FIBRE
F: ADENOVIRUS FIBRE


Theoretical massNumber of molelcules
Total (without water)171,5266
Polymers171,5266
Non-polymers00
Water10,431579
1
A: ADENOVIRUS FIBRE
B: ADENOVIRUS FIBRE
C: ADENOVIRUS FIBRE


Theoretical massNumber of molelcules
Total (without water)85,7633
Polymers85,7633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: ADENOVIRUS FIBRE
E: ADENOVIRUS FIBRE
F: ADENOVIRUS FIBRE


Theoretical massNumber of molelcules
Total (without water)85,7633
Polymers85,7633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)165.510, 95.870, 211.770
Angle α, β, γ (deg.)90.00, 106.83, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE MOLECULE CONSISTS IS A HOMO- TRIMER.CHAINS A, B AND C FORM ONE TRIMER CHAINS D, E AND F THE OTHER TRIMER

-
Components

#1: Protein
ADENOVIRUS FIBRE


Mass: 28587.725 Da / Num. of mol.: 6
Fragment: FRAGMENT CONTAINING THE FOUR DISTAL SHAFT REPEATS PLUS THE HEAD DOMAIN.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN ADENOVIRUS 2 / Gene: LOCUS AD2H2 / Plasmid: PT7.7 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P03275
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.6 Å3/Da / Density % sol: 73 %
Crystal growpH: 4
Details: 0.8 M AMMONIUM SULPHATE, 100 MM SODIUM CITRATE, PH 4.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
20.8 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.948
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 103327 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.132 / Net I/σ(I): 4.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.287 / % possible all: 54.9
Reflection
*PLUS
Rmerge(I) obs: 0.132
Reflection shell
*PLUS
% possible obs: 59.9 % / Num. unique obs: 10696 / Rmerge(I) obs: 0.287

-
Processing

Software
NameVersionClassification
CNS0.4refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QHV

1qhv


Resolution: 2.4→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2480815.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1662 1.6 %SHELLS
Rwork0.232 ---
obs0.232 103325 84 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å25.19 Å2
2---3.52 Å20 Å2
3---5.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12042 0 0 579 12621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.53 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.365 208 2.2 %
Rwork0.312 9430 -
obs--54.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor obs: 0.312

+
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