[English] 日本語
Yorodumi
- PDB-3exw: Crystal structure of the human Adenovirus type 7 fiber knob -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3exw
TitleCrystal structure of the human Adenovirus type 7 fiber knob
ComponentsL5 fiber protein
KeywordsVIRAL PROTEIN / adenovirus / trimer / fiber knob / ad7 / ads
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
Fiber protein / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 7
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L5 fiber protein
B: L5 fiber protein
C: L5 fiber protein


Theoretical massNumber of molelcules
Total (without water)70,4683
Polymers70,4683
Non-polymers00
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-36 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.310, 88.050, 79.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

-
Components

#1: Protein L5 fiber protein


Mass: 23489.217 Da / Num. of mol.: 3 / Fragment: residues 117-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Strain: Gomen / Gene: L5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q5EY45, UniProt: P15141*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 23% w/v PEG 3350, 0.1M HEPES buffer, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2006
RadiationMonochromator: Undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→79.06 Å / Num. all: 59433 / Num. obs: 52966 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rsym value: 0.05
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.34 / Rsym value: 0.364 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.3.0037refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Adenovirus type 11 fiber knob

Resolution: 1.75→36.11 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.906 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22999 5916 10 %RANDOM
Rwork0.19192 ---
obs0.19572 52966 99.08 %-
all-59433 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.948 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---1.03 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 0 492 5128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224743
X-RAY DIFFRACTIONr_bond_other_d0.0030.022957
X-RAY DIFFRACTIONr_angle_refined_deg0.7321.9326497
X-RAY DIFFRACTIONr_angle_other_deg0.65137281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.095601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47225.217207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44115739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2721512
X-RAY DIFFRACTIONr_chiral_restr0.0540.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02944
X-RAY DIFFRACTIONr_nbd_refined0.2120.2871
X-RAY DIFFRACTIONr_nbd_other0.2180.23280
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22382
X-RAY DIFFRACTIONr_nbtor_other0.0840.22463
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2420
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.211
X-RAY DIFFRACTIONr_mcbond_it0.9831.53826
X-RAY DIFFRACTIONr_mcbond_other0.1731.51196
X-RAY DIFFRACTIONr_mcangle_it1.14424874
X-RAY DIFFRACTIONr_scbond_it1.69532096
X-RAY DIFFRACTIONr_scangle_it2.3654.51618
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2505 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.050.05
tight thermal0.170.5
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 441 -
Rwork0.278 3701 -
obs--94.5 %

+
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