[English] 日本語
Yorodumi
- PDB-5g5o: Structure of the snake adenovirus 1 hexon-interlacing LH3 protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g5o
TitleStructure of the snake adenovirus 1 hexon-interlacing LH3 protein, native
ComponentsLH3 HEXON-INTERLACING CAPSID PROTEIN
KeywordsVIRAL PROTEIN / CAPSID PROTEIN / BETA-HELIX
Function / homologyPectin lyase fold / Pectin lyase fold/virulence factor / virion component / ACETATE ION / Hexon-interlacing protein LH3
Function and homology information
Biological speciesSNAKE ADENOVIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNguyen, T.H. / Singh, A.K. / Albala-Perez, B. / van Raaij, M.J.
CitationJournal: Structure / Year: 2017
Title: Structure of a Reptilian Adenovirus Reveals a Phage Tailspike Fold Stabilizing a Vertebrate Virus Capsid.
Authors: Rosa Menéndez-Conejero / Thanh H Nguyen / Abhimanyu K Singh / Gabriela N Condezo / Rachel E Marschang / Mark J van Raaij / Carmen San Martín /
Abstract: Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural ...Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural studies on the complete virion of any AdV with a non-mammalian host. We combine mass spectrometry, cryo-electron microscopy, and protein crystallography to characterize the composition and structure of a snake AdV (SnAdV-1, Atadenovirus genus). SnAdV-1 particles contain the genus-specific proteins LH3, p32k, and LH2, a previously unrecognized structural component. Remarkably, the cementing protein LH3 has a trimeric β helix fold typical of bacteriophage host attachment proteins. The organization of minor coat proteins differs from that in human AdVs, correlating with higher thermostability in SnAdV-1. These findings add a new piece to the intriguing puzzle of virus evolution, hint at the use of cell entry pathways different from those in human AdVs, and will help development of new, thermostable SnAdV-1-based vectors.
History
DepositionMay 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LH3 HEXON-INTERLACING CAPSID PROTEIN
B: LH3 HEXON-INTERLACING CAPSID PROTEIN
C: LH3 HEXON-INTERLACING CAPSID PROTEIN
D: LH3 HEXON-INTERLACING CAPSID PROTEIN
E: LH3 HEXON-INTERLACING CAPSID PROTEIN
F: LH3 HEXON-INTERLACING CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,04731
Polymers241,4486
Non-polymers1,59925
Water27,4731525
1
D: LH3 HEXON-INTERLACING CAPSID PROTEIN
E: LH3 HEXON-INTERLACING CAPSID PROTEIN
F: LH3 HEXON-INTERLACING CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,64517
Polymers120,7243
Non-polymers92114
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13300 Å2
ΔGint-58.8 kcal/mol
Surface area28930 Å2
MethodPISA
2
A: LH3 HEXON-INTERLACING CAPSID PROTEIN
B: LH3 HEXON-INTERLACING CAPSID PROTEIN
C: LH3 HEXON-INTERLACING CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,40214
Polymers120,7243
Non-polymers67811
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-56.1 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.790, 126.880, 120.940
Angle α, β, γ (deg.)90.00, 106.15, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
LH3 HEXON-INTERLACING CAPSID PROTEIN


Mass: 40241.266 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SNAKE ADENOVIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): JM109 / References: UniProt: A9CB85
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1525 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWE FOUND SEVERAL SEQUENCE DIFFERENCES BETWEEN OUR PCR- AMPLIFIED GENE AND THE DATABASE. HOWEVER, WE ...WE FOUND SEVERAL SEQUENCE DIFFERENCES BETWEEN OUR PCR- AMPLIFIED GENE AND THE DATABASE. HOWEVER, WE CONFIRMED OUR SEQUENCE IS CORRECT BY MASS SPECTROMETRY. THE EXPRESSED PROTEIN CONTAINS AN N-TERMINAL EXPRESSION AND PURIFICATION TAG, WHICH MAY OR MAY NOT HAVE BEEN CLEAVED OFF DURING THE CRYSTALLIZATION PROCESS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.3 % / Description: NONE
Crystal growpH: 8.5
Details: 10 MM TRIS-HCL PH 8.5, 20% (W/V) PEG3350, 0.2 M AMMONIUM ACETATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2013
Details: TWO CYLINDRICAL PARABOLIC VERTICAL FOCUSSING MIRRORS
RadiationMonochromator: DOUBLE SI(111) CRYSTAL FIXED-EXIT BRAGG MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 130350 / % possible obs: 94.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.4 / % possible all: 87.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G5N

5g5n


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.131 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY, RESIDUES 156-162 FROM CHAINS A, D AND F, AND 156-161 FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY, RESIDUES 156-162 FROM CHAINS A, D AND F, AND 156-161 FROM CHAIN C ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22569 1945 1.5 %RANDOM
Rwork0.17224 ---
obs0.17305 128200 94.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.767 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-1.44 Å2
2--0.72 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15535 0 98 1525 17158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916006
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214696
X-RAY DIFFRACTIONr_angle_refined_deg1.451.92921746
X-RAY DIFFRACTIONr_angle_other_deg0.925333594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88252041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.05224.085754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.289152293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.45415101
X-RAY DIFFRACTIONr_chiral_restr0.0830.22320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023997
X-RAY DIFFRACTIONr_nbd_refined0.2030.28780
X-RAY DIFFRACTIONr_nbd_other0.1550.229322
X-RAY DIFFRACTIONr_nbtor_refined0.170.215158
X-RAY DIFFRACTIONr_nbtor_other0.0710.216120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2930
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0380.212
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.279
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1182.0728202
X-RAY DIFFRACTIONr_mcbond_other1.1162.0718190
X-RAY DIFFRACTIONr_mcangle_it1.8333.09810223
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2962.1987804
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.153.24811523
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 140 -
Rwork0.303 8709 -
obs--87.08 %

+
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://pdbjlvh1.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