[English] 日本語
Yorodumi
- PDB-1cjd: THE BACTERIOPHAGE PRD1 COAT PROTEIN, P3, IS STRUCTURALLY SIMILAR ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cjd
TitleTHE BACTERIOPHAGE PRD1 COAT PROTEIN, P3, IS STRUCTURALLY SIMILAR TO HUMAN ADENOVIRUS HEXON
ComponentsPROTEIN (MAJOR CAPSID PROTEIN (P3))
KeywordsVIRAL PROTEIN / BACTERIOPHAGE PRD1 / COAT PROTEIN / JELLY ROLL
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 / 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 / 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 / MAD / Resolution: 1.85 Å
AuthorsBenson, S.D. / Bamford, J.K.H. / Bamford, D.H. / Burnett, R.M.
Citation
Journal: Cell / Year: 1999
Title: Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures.
Authors: S D Benson / J K Bamford / D H Bamford / R M Burnett /
Abstract: The unusual bacteriophage PRD1 features a membrane beneath its icosahedral protein coat. The crystal structure of the major coat protein, P3, at 1.85 A resolution reveals a molecule with three ...The unusual bacteriophage PRD1 features a membrane beneath its icosahedral protein coat. The crystal structure of the major coat protein, P3, at 1.85 A resolution reveals a molecule with three interlocking subunits, each with two eight-stranded viral jelly rolls normal to the viral capsid, and putative membrane-interacting regions. Surprisingly, the P3 molecule closely resembles hexon, the equivalent protein in human adenovirus. Both viruses also have similar overall architecture, with identical capsid lattices and attachment proteins at their vertices. Although these two dsDNA viruses infect hosts from very different kingdoms, their striking similarities, from major coat protein through capsid architecture, strongly suggest their evolutionary relationship.
#1: 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.
#2: Journal: Virology / Year: 1990
Title: Capsomer proteins of bacteriophage PRD1, a bacterial virus with a membrane.
Authors: Bamford, J.K. / Bamford, D.H.
History
DepositionApr 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (MAJOR CAPSID PROTEIN (P3))
B: PROTEIN (MAJOR CAPSID PROTEIN (P3))
C: PROTEIN (MAJOR CAPSID PROTEIN (P3))


Theoretical massNumber of molelcules
Total (without water)130,0393
Polymers130,0393
Non-polymers00
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-52 kcal/mol
Surface area40420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.956, 121.296, 126.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.099073, 0.989728, 0.102942), (-0.01345, -0.102161, 0.99471), (0.994959, -0.09996, 0.003165)-11.2353, 4.0649, 8.6096
2given(0.098976, -0.013544, 0.995086), (0.989644, -0.103222, -0.099896), (0.104089, 0.994549, 0.003195)-7.4965, 12.566, -3.0997

-
Components

#1: Protein PROTEIN (MAJOR CAPSID 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) / References: UniProt: P22535
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 64 %
Description: MAD PHASES WERE COLLECTED ON A SE-MET P3 DERIVATIVE AND THE MODEL USED TO PHASE THE NATIVE P3 DATA
Crystal growpH: 4.2
Details: 35% (W/V) MPD, 0.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.2
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMTris-HCl1drop
3300 mM1dropNaCl
435 %(v/v)MPD1reservoir
5100 mMsodium acetate1reservoir
6200 mM1reservoirNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9500, 0.9786, 0.9790
DetectorType: BRANDEIS / Detector: CCD / Date: Jun 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97861
30.9791
ReflectionResolution: 1.85→35 Å / Num. obs: 151224 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 10.1 Å2 / Rsym value: 0.046 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2 % / Mean I/σ(I) obs: 9 / Rsym value: 0.197 / % possible all: 91.6
Reflection
*PLUS
Rmerge(I) obs: 0.046

-
Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→35 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1372 1.1 %SPHERES
Rwork0.178 ---
obs-121093 78.3 %-
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.85→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8502 0 0 473 8975
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.85
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.561.5
X-RAY DIFFRACTIONx_mcangle_it2.532
X-RAY DIFFRACTIONx_scbond_it2.722
X-RAY DIFFRACTIONx_scangle_it4.172.5
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 1.85→1.93 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2 100 1.1 %
Rwork0.196 8869 -
obs--46.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35 Å / σ(F): 2 / % reflection Rfree: 1.1 % / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.85
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.2 / % reflection Rfree: 1.1 % / Rfactor Rwork: 0.196

+
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