[English] 日本語
Yorodumi
- PDB-4bbb: THE STRUCTURE OF VACCINIA VIRUS N1 Q61Y MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bbb
TitleTHE STRUCTURE OF VACCINIA VIRUS N1 Q61Y MUTANT
ComponentsN1L
KeywordsVIRAL PROTEIN / BCL-LIKE PROTEIN / APOPTOSIS / VIRULENCE FACTOR
Function / homology
Function and homology information


symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host NF-kappaB cascade / :
Similarity search - Function
Orthopoxvirus, Protein N1 / dsDNA poxvirus / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / Apoptosis Regulator Bcl-x / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein OPG035 / Uncharacterized protein
Similarity search - Component
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsMaluquer de Motes, C. / Cooray, S. / McGourty, K. / Ren, H. / Bahar, M.W. / Stuart, D.I. / Grimes, J.M. / Graham, S.C. / Smith, G.L.
CitationJournal: Plos Pathog. / Year: 2011
Title: Inhibition of Apoptosis and NF-kappaB Activation by Vaccinia Protein N1 Occur Via Distinct Binding Surfaces and Make Different Contributions to Virulence.
Authors: Maluquer De Motes, C. / Cooray, S. / Ren, H. / Almeida, G.M.F. / Mcgourty, K. / Bahar, M.W. / Stuart, D.I. / Grimes, J.M. / Graham, S.C. / Smith, G.L.
History
DepositionSep 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N1L
B: N1L
C: N1L
D: N1L
E: N1L
F: N1L


Theoretical massNumber of molelcules
Total (without water)90,4096
Polymers90,4096
Non-polymers00
Water00
1
B: N1L
E: N1L


Theoretical massNumber of molelcules
Total (without water)30,1362
Polymers30,1362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-4.8 kcal/mol
Surface area11500 Å2
MethodPISA
2
A: N1L
F: N1L


Theoretical massNumber of molelcules
Total (without water)30,1362
Polymers30,1362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-3.8 kcal/mol
Surface area11570 Å2
MethodPISA
3
C: N1L
D: N1L


Theoretical massNumber of molelcules
Total (without water)30,1362
Polymers30,1362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-3.9 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.718, 109.848, 70.346
Angle α, β, γ (deg.)90.00, 110.85, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
N1L / N1L PROTEIN / VACV-DUKE-037 / VACV026 / VIROKINE


Mass: 15068.172 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C40S MUTATION WAS INTRODUCED TO AVOID INTERMOLECULAR DISULPHIDE BOND DRIVEN AGGREGATION.
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q49PX0, UniProt: P21054*PLUS
Sequence detailsQ61Y IS FUNCTIONAL MUTATION. C40S MUTATION WAS INTRODUCED TO AVOID INTERMOLECULAR DISULPHIDE BOND ...Q61Y IS FUNCTIONAL MUTATION. C40S MUTATION WAS INTRODUCED TO AVOID INTERMOLECULAR DISULPHIDE BOND DRIVEN AGGREGATION (AS PDB ID 2UXE). C-TERMINAL LEHHHHHH SEQUENCE DERIVES FROM EXPRESSION VECTOR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.82 %
Description: SOLVED BY ISOMORPHOUS DIFFERENCE FOURIER SYNTHESIS.
Crystal growpH: 7 / Details: pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2008 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: ASYMMETRIC LAUE 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.1→42.2 Å / Num. obs: 18168 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 105.85 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3
Reflection shellResolution: 3.09→3.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2I39

2i39


Resolution: 3.09→42.15 Å / Cor.coef. Fo:Fc: 0.9558 / Cor.coef. Fo:Fc free: 0.9365 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 918 5.06 %RANDOM
Rwork0.1784 ---
obs0.1802 18134 --
Displacement parametersBiso mean: 106.37 Å2
Baniso -1Baniso -2Baniso -3
1-11.7651 Å20 Å2-13.9888 Å2
2---3.7355 Å20 Å2
3----8.0296 Å2
Refine analyzeLuzzati coordinate error obs: 0.773 Å
Refinement stepCycle: LAST / Resolution: 3.09→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5703 0 0 0 5703
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015790HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.017806HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2166SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes179HARMONIC2
X-RAY DIFFRACTIONt_gen_planes803HARMONIC5
X-RAY DIFFRACTIONt_it5790HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion20.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion763SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7055SEMIHARMONIC4
LS refinement shellResolution: 3.09→3.28 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2979 150 5.31 %
Rwork0.2541 2676 -
all0.2566 2826 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.1173-0.0466-1.97257.3897-1.2188.4468-0.30930.9124-0.6304-1.07410.41790.57411.116-0.3594-0.1085-0.1062-0.0793-0.2123-0.0684-0.07740.039835.3762-14.5769-16.7133
25.572-0.3064-0.91657.2942-2.96157.6326-0.21990.0893-0.22940.58950.36690.8318-0.151-1.3745-0.147-0.1341-0.11290.3037-0.1857-0.06040.354812.533530.687-15.7351
39.0283-0.4278-3.57425.40990.96776.71710.76090.69781.157-0.8255-0.1317-0.4795-1.0125-0.2478-0.6292-0.0041-0.11750.1818-0.09920.0610.023-3.15367.1696-30.192
45.6257-1.078-2.51948.19512.31418.0919-0.2237-1.2087-0.4191.15130.1572-0.51520.82650.97990.0664-0.1268-0.0376-0.13710.29510.055-0.01045.9182-9.7547-16.8053
55.5784-0.331-0.54064.74320.73986.84340.00780.3083-0.3312-0.0896-0.0106-0.48870.25880.70560.0028-0.0507-0.01730.2037-0.3042-0.06630.353335.39726.706-17.3782
68.56260.2038-2.12325.5278-0.20715.0780.6939-1.19740.85560.8336-0.09840.533-0.86870.4723-0.5955-0.0766-0.06090.13310.0041-0.17470.053739.90544.6526-4.4987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1-114
2X-RAY DIFFRACTION2CHAIN B AND RESID 1-114
3X-RAY DIFFRACTION3CHAIN C AND RESID 1-114
4X-RAY DIFFRACTION4CHAIN D AND RESID 1-114
5X-RAY DIFFRACTION5CHAIN E AND RESID 1-114
6X-RAY DIFFRACTION6CHAIN F AND RESID 1-114

+
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