[English] 日本語
Yorodumi
- PDB-1js9: Brome Mosaic Virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1js9
TitleBrome Mosaic Virus
ComponentsCoat protein
KeywordsVIRUS / PLANT VIRUS / CAPSID PROTEIN / COAT PROTEIN / BROMOVIRUSES / BMV / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell endoplasmic reticulum / viral nucleocapsid / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Satellite virus coat domain / Bromovirus coat protein / Bromovirus coat protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBrome mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLucas, R.W. / Larson, S.B. / McPherson, A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: The crystallographic structure of brome mosaic virus.
Authors: Lucas, R.W. / Larson, S.B. / McPherson, A.
#1: Journal: Virology / Year: 2001
Title: Crystallization of Brome Mosaic Virus and T=1 Brome Mosaic Virus Particles Following a Structural Transition
Authors: Lucas, R.W. / Kuznetsov, Y.G. / Larson, S.B. / McPherson, A.
History
DepositionAug 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Other
Revision 1.4Feb 17, 2016Group: Non-polymer description
Revision 1.5Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.name / _software.type / _software.version
Revision 1.6Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _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.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_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: Coat protein
B: Coat protein
C: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5666
Polymers61,2353
Non-polymers3313
Water0
1
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,693,931360
Polymers3,674,075180
Non-polymers19,856180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 5


  • icosahedral pentamer
  • 308 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)307,82830
Polymers306,17315
Non-polymers1,65515
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 369 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)369,39336
Polymers367,40718
Non-polymers1,98618
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.23 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,231,310120
Polymers1,224,69260
Non-polymers6,61960
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)269.244, 269.244, 638.136
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5590482, -0.78943463, 0.25349176), (0.72226366, 0.31352837, -0.61646992), (0.40718584, 0.52772429, 0.74545742)
3generate(-0.15442681, -0.5550684, 0.81734413), (0.37921252, -0.79720606, -0.469745), (0.9123323, 0.23740591, 0.33359888)
4generate(-0.15442681, 0.37921252, 0.9123323), (-0.5550684, -0.79720606, 0.23740591), (0.81734413, -0.469745, 0.33359888)
5generate(0.5590482, 0.72226366, 0.40718584), (-0.78943463, 0.31352837, 0.52772429), (0.25349176, -0.61646992, 0.74545742)
6generate(-0.0029028, 0.57857882, 0.81562131), (0.57857882, -0.66427199, 0.47327504), (0.81562131, 0.47327504, -0.33282521)
7generate(0.74837311, 0.61411562, 0.25059868), (0.03638482, -0.41525954, 0.90897506), (0.66227928, -0.6711345, -0.33311356)
8generate(0.96397027, -0.26600197, -0.00206675), (0.09053577, 0.32076913, 0.94282047), (-0.25012915, -0.90903802, 0.33329459)
9generate(0.34594074, -0.84548135, 0.40680006), (0.66619689, 0.52664741, 0.52803807), (-0.66068654, 0.08833906, 0.74544584)
10generate(-0.25161969, -0.32350171, 0.91215907), (0.96782409, -0.08214148, 0.23784304), (-0.00201653, 0.94265551, 0.33376117)
11generate(-0.99999399, -0.00283072, 0.00200069), (-0.00283072, 0.33374358, -0.94265965), (0.00200069, -0.94265965, -0.33374959)
12generate(-0.56027471, 0.78959819, -0.25025376), (-0.14436931, -0.39059164, -0.90917307), (-0.81562844, -0.47325772, 0.33283236)
13generate(0.15517773, 0.55779671, -0.81534208), (-0.73302195, -0.48828414, -0.47355825), (-0.66226784, 0.67114934, 0.33310641)
14generate(0.15763237, -0.37789339, -0.91233142), (-0.95529071, 0.1756738, -0.23782005), (0.25014335, 0.90902987, -0.33330617)
15generate(-0.55630301, -0.7243802, -0.40718581), (-0.50400771, 0.68371487, -0.52774066), (0.66068388, -0.08835893, -0.74544585)
16generate(0.0028968, -0.5757481, -0.817622), (-0.5757481, -0.66947159, 0.4693846), (-0.817622, 0.4693846, -0.3334252)
17generate(-0.74714659, -0.61427918, -0.25383668), (-0.61427918, 0.49232281, 0.61666793), (-0.25383668, 0.61666793, -0.74517622)
18generate(-0.96472119, 0.26327366, 6.469E-5), (0.26327366, 0.96472107, 0.00048277), (6.469E-5, 0.00048277, -0.99999988)
19generate(-0.3491463, 0.84416222, -0.40680094), (0.84416222, 0.09488485, -0.52762393), (-0.40680094, -0.52762393, -0.74573855)
20generate(0.2488745, 0.32561825, -0.91215911), (0.32561825, -0.91510176, -0.23782666), (-0.91215911, -0.23782666, -0.33377274)

-
Components

#1: Protein Coat protein / Capsid protein


Mass: 20411.525 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Brome mosaic virus / Genus: Bromovirus / Strain: Dickson / References: UniProt: P03602
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.837 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: PEG 550, magnesium acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17. mg/mlvirus1drop
223 %PEG550 MME1reservoir
30.1 Mmagnesium acetate1reservoirpH5.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 28, 2000
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 3.4→39.79 Å / Num. all: 203504 / Num. obs: 203504 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Limit h max: 68 / Limit h min: -67 / Limit k max: 79 / Limit k min: -67 / Limit l max: 182 / Limit l min: 0 / Observed criterion F max: 100033.62 / Observed criterion F min: 0.32 / Rsym value: 0.17 / Net I/σ(I): 3.02
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 1.34 % / Mean I/σ(I) obs: 0.58 / Num. unique all: 610 / % possible all: 55.4
Reflection
*PLUS
Highest resolution: 3.4 Å / % possible obs: 86.4 % / Num. measured all: 2463817 / Rmerge(I) obs: 0.17

-
Processing

Software
NameVersionClassificationNB
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CWP

1cwp


Resolution: 3.4→39.7 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
Details: SIMULATED ANNEALING AND CONJUGATE GRADIENT MINIMIZATION
RfactorNum. reflection% reflectionSelection details
Rfree0.25 5118 5 %RANDOM
Rwork0.238 ---
all0.428 203504 --
obs0.24 102537 50.3 %-
Solvent computationSolvent model: XPLOR bulk solvent model used / Bsol: 300 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 327.61 Å2 / Biso mean: 102.3 Å2 / Biso min: 0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a1.08 Å0.8 Å
Luzzati d res high-3.4
Refinement stepCycle: LAST / Resolution: 3.4→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 21 0 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d29.7
X-RAY DIFFRACTIONx_improper_angle_d0.69
X-RAY DIFFRACTIONx_mcbond_it13.378.5
X-RAY DIFFRACTIONx_mcangle_it19.989
X-RAY DIFFRACTIONx_scbond_it33.9615.5
X-RAY DIFFRACTIONx_scangle_it46.8916
Refine LS restraints NCSNCS model details: Constraints for icosahedral symmetry and restraints for 8 beta strands between A, B, and C subunits
Rms dev Biso : 1.48 Å2 / Rms dev position: 0.16 Å / Weight Biso : 1 / Weight position: 300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.4-3.520.3987286.90.41543760.075296766161.7
3.56-3.740.3641215.20.33822270.0332965823487.9
3.74-3.980.2933085.30.31154720.01729621578019.5
3.98-4.280.2964264.60.28888330.01429684925931.2
4.28-4.710.2768745.10.265161400.009296341701457.4
4.71-5.390.26899150.245188490.009296161984067
5.39-6.790.244111450.235211440.007296182225875.2
6.79-39.790.22512434.90.218240700.006296372531385.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2mg_xplor_par.txtPEG_xplor_top.txt
X-RAY DIFFRACTION3PEG_xplor_par.txtion.top
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 4 Å / Rfactor obs: 0.237 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.49
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.69

+
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