[English] 日本語
Yorodumi
- PDB-1hx6: P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hx6
TitleP3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1.
ComponentsMAJOR CAPSID PROTEIN
KeywordsVIRAL PROTEIN / bacteriophage PRD1 / coat protein / jelly roll / viral beta barrel
Function / homology
Function and homology information


Viral coat protein p3 / Adenovirus Type 2 Hexon; domain 4 / Bacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal / P3 major capsid protein N-terminal / Group II dsDNA virus coat/capsid protein / Jelly Rolls - #20 / Distorted Sandwich / Viral coat protein subunit / Jelly Rolls ...Viral coat protein p3 / Adenovirus Type 2 Hexon; domain 4 / Bacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal / P3 major capsid protein N-terminal / Group II dsDNA virus coat/capsid protein / Jelly Rolls - #20 / Distorted Sandwich / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major capsid protein P3
Similarity search - Component
Biological speciesEnterobacteria phage PRD1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBenson, S.D. / Bamford, J.K.H. / Bamford, D.H. / Burnett, R.M.
Citation
Journal: Acta Crystallogr D Biol Crystallogr / Year: 2002
Title: The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 A resolution.
Authors: Stacy D Benson / Jaana K H Bamford / Dennis H Bamford / Roger M Burnett /
Abstract: P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now ...P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now been extended to 1.65 A resolution (R(work) = 19.0% and R(free) = 20.8%). The new high-resolution model shows that P3 forms crystals through hydrophobic patches solvated by 2-methyl-2,4-pentanediol molecules. It reveals details of how the molecule's high stability may be achieved through ordered solvent in addition to intra- and intersubunit interactions. Of particular importance is a 'puddle' at the top of the molecule containing a four-layer deep hydration shell that cross-links a complex structural feature formed by 'trimerization loops'. These loops also link subunits by extending over a neighbor to reach the third subunit in the trimer. As each subunit has two eight-stranded viral jelly rolls, the trimer has a pseudo-hexagonal shape to allow close packing in its 240 hexavalent capsid positions. Flexible regions in P3 facilitate these interactions within the capsid and with the underlying membrane. A selenometh-ionine P3 derivative, with which the structure was solved, has been refined to 2.2 A resolution (R(work) = 20.1% and R(free) = 22.8%). The derivatized molecule is essentially unchanged, although synchrotron radiation has the curious effect of causing it to rotate about its threefold axis. P3 is a second example of a trimeric 'double-barrel' protein that forms a stable building block with optimal shape for constructing a large icosahedral viral capsid. A major difference is that hexon has long variable loops that distinguish different adenovirus species. The short loops in P3 and the severe constraints of its various interactions explain why the PRD1 family has highly conserved coat proteins.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Viral Evolution Revealed by Bacteriophage PRD1 and Human Adenovirus Coat Protein Structures
Authors: Benson, S.D. / Bamford, J.K. / Bamford, D.H. / Burnett, R.M.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of the Major Coat Protein of PRD1, a Bacteriophage with an Internal Membrane
Authors: Stewart, P.L. / Ghosh, S. / Bamford, D.H. / Burnett, R.M.
#3: Journal: Virology / Year: 1990
Title: Capsomer Proteins of Bacteriophage PRD1, a Bacterial Virus with a Membrane
Authors: Bamford, J.K. / Bamford, D.H.
#4: Journal: MOL.THER. / Year: 2000
Title: Type-specific Epitope Locations Revealed by X-ray Crystallographic Study of Adenovirus Type 5 Hexon
Authors: Rux, J.J. / Burnett, R.M.
History
DepositionJan 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,39830
Polymers130,0393
Non-polymers2,35927
Water14,088782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17130 Å2
ΔGint-305 kcal/mol
Surface area41020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.960, 121.300, 126.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MAJOR CAPSID PROTEIN / PROTEIN P3


Mass: 43346.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage PRD1 (virus) / Genus: Tectivirus / Production host: Salmonella typhimurium (bacteria) / Strain (production host): DS88 / References: UniProt: P22535
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 3.48 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 30% MPD, 0.1 M sodium acetate, 0.2 M NaCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Jun 11, 1997 / Details: mirrors
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.6→87 Å / Num. obs: 195631 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 4.7 / Net I/σ(I): 20
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 1.5 % / Num. unique all: 8530 / Rsym value: 40.3 / % possible all: 61.2

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: selenomethionine P3 - PDB entry 1HQN

1hqn


Resolution: 1.65→53.45 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 360397.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2072 1.2 %SPHERES
Rwork0.19 ---
obs0.19 179469 82.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.85 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20 Å2
2---0.07 Å20 Å2
3----1.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.65→53.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9091 0 9 926 10026
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it1.52
X-RAY DIFFRACTIONc_scangle_it2.192.5
LS refinement shellResolution: 1.65→1.71 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.284 123 1.2 %
Rwork0.31 9813 -
obs-7482 46.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MPD.PARAMMPD.TOP

+
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