[English] 日本語
Yorodumi
- PDB-5nc1: Structure of the distal domain of mouse adenovirus 2 fibre bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nc1
TitleStructure of the distal domain of mouse adenovirus 2 fibre bound to N-acetyl-glucosamine
ComponentsFiber
KeywordsVIRAL PROTEIN / Triple beta-spiral / 3-bladed propeller / ABCJ-GHID topology / N-acetyl-glucosamine binding
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
Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily
Similarity search - Domain/homology
Biological speciesMurine adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSingh, A.K. / van Raaij, M.J.
CitationJournal: J. Gen. Virol. / Year: 2018
Title: Structure and N-acetylglucosamine binding of the distal domain of mouse adenovirus 2 fibre.
Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S. ...Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S.S. / Bromme, B.A. / Smith, J.G. / van Raaij, M.J.
History
DepositionMar 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _entity.formula_weight
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fiber
B: Fiber
C: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,24518
Polymers77,4333
Non-polymers1,81215
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Protein is trimeric on SDS-PAGE when sample is not boiled prior to analysis.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint-201 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.410, 163.410, 163.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11C-932-

HOH

21C-980-

HOH

-
Components

#1: Protein Fiber


Mass: 25810.922 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEF is an expression and purification tag. GALTAQGAS residues are disordered.
Source: (gene. exp.) Murine adenovirus 2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E7CH51
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.125 M lithium sulphate, 0.075 M HEPES-NaOH, 25% (v/v) glycerol, 10 mM Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2→28.9 Å / Num. obs: 48930 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3642 / CC1/2: 0.714 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NBH

5nbh


Resolution: 2→28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.794 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.137 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20513 2409 4.9 %RANDOM
Rwork0.16538 ---
obs0.16736 46439 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.478 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 106 350 4953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024794
X-RAY DIFFRACTIONr_bond_other_d0.0020.024223
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9776543
X-RAY DIFFRACTIONr_angle_other_deg0.85939842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30623.854205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14115759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5421524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021018
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7372.7562346
X-RAY DIFFRACTIONr_mcbond_other1.7372.7552345
X-RAY DIFFRACTIONr_mcangle_it2.8864.1212936
X-RAY DIFFRACTIONr_mcangle_other2.8864.1222937
X-RAY DIFFRACTIONr_scbond_it2.13.052448
X-RAY DIFFRACTIONr_scbond_other2.13.052448
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3754.4893594
X-RAY DIFFRACTIONr_long_range_B_refined5.79633.1585039
X-RAY DIFFRACTIONr_long_range_B_other5.66332.914976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 165 -
Rwork0.269 3444 -
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