[English] 日本語
Yorodumi
- PDB-3f0y: Crystal structure of the human Adenovirus type 14 fiber knob -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f0y
TitleCrystal structure of the human Adenovirus type 14 fiber knob
ComponentsFiber protein
KeywordsVIRAL PROTEIN / adenovirus / Ad14 / CD46 / trimer / fiber / knob
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
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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Fiber protein
Similarity search - Component
Biological speciesHuman adenovirus 14
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPersson, B.D. / Reiter, D.M. / Arnberg, N. / Stehle, T.
CitationJournal: J.Virol. / Year: 2009
Title: An arginine switch in the species B adenovirus knob determines high-affinity engagement of cellular receptor CD46
Authors: Persson, B.D. / Muller, S. / Reiter, D.M. / Schmitt, B.B. / Marttila, M. / Sumowski, C.V. / Schweizer, S. / Scheu, U. / Ochsenfeld, C. / Arnberg, N. / Stehle, T.
History
DepositionOct 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fiber protein
B: Fiber protein
C: Fiber protein
D: Fiber protein
E: Fiber protein
F: Fiber protein
G: Fiber protein
H: Fiber protein
I: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,86916
Polymers207,2939
Non-polymers5767
Water32,4811803
1
A: Fiber protein
B: Fiber protein
C: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5819
Polymers69,0983
Non-polymers4846
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-26 kcal/mol
Surface area22090 Å2
MethodPISA
2
D: Fiber protein
E: Fiber protein
F: Fiber protein


Theoretical massNumber of molelcules
Total (without water)69,0983
Polymers69,0983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-36 kcal/mol
Surface area22220 Å2
MethodPISA
3
G: Fiber protein
H: Fiber protein
I: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1904
Polymers69,0983
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-38 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.470, 106.470, 311.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-1323-

HOH

21F-797-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12I
22A
/ NCS ensembles :
ID
1
2

-
Components

#1: Protein
Fiber protein


Mass: 23032.607 Da / Num. of mol.: 9 / Fragment: resdiues 123-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 14 / Strain: De Wit / Gene: Fiber, L5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q8V791
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1803 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20% (w/v) PEG 8000, 0.1M CHES, 200mM NaCl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2007
RadiationMonochromator: Undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.4 Å / Num. all: 187138 / Num. obs: 185386 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.078
Reflection shellResolution: 1.8→1.9 Å / % possible all: 94.4

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.3.0037refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Adenovirus type 11 fiber knob

Resolution: 1.8→47.4 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.745 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21495 9272 5 %RANDOM
Rwork0.18803 ---
obs0.18937 176156 100 %-
all-176156 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13904 0 39 1803 15746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02214416
X-RAY DIFFRACTIONr_bond_other_d0.0010.029131
X-RAY DIFFRACTIONr_angle_refined_deg0.9261.93119716
X-RAY DIFFRACTIONr_angle_other_deg0.748322375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92951826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41624.903667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.937152246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8351555
X-RAY DIFFRACTIONr_chiral_restr0.0570.22283
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022956
X-RAY DIFFRACTIONr_nbd_refined0.1670.22632
X-RAY DIFFRACTIONr_nbd_other0.1780.210634
X-RAY DIFFRACTIONr_nbtor_refined0.170.27347
X-RAY DIFFRACTIONr_nbtor_other0.0790.27544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.21978
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.246
X-RAY DIFFRACTIONr_mcbond_it0.4391.511588
X-RAY DIFFRACTIONr_mcbond_other0.0391.53602
X-RAY DIFFRACTIONr_mcangle_it0.485214656
X-RAY DIFFRACTIONr_scbond_it0.58436465
X-RAY DIFFRACTIONr_scangle_it0.864.55035
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B127tight positional0.010.05
2I45medium positional0.240.5
1B127tight thermal0.040.5
2I45medium thermal0.092
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 637 -
Rwork0.25 12099 -
obs--100 %

+
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