[English] 日本語
Yorodumi
- PDB-1w5j: AN ANTI-PARALLEL FOUR HELIX BUNDLE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w5j
TitleAN ANTI-PARALLEL FOUR HELIX BUNDLE
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsFOUR HELIX BUNDLE / ANTIPARALLEL FOUR HELIX BUNDLE
Function / homology
Function and homology information


nitrogen catabolite activation of transcription from RNA polymerase II promoter / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...nitrogen catabolite activation of transcription from RNA polymerase II promoter / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
: / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYadav, M.K. / Leman, L.J. / Stout, C.D. / Ghadiri, M.R.
CitationJournal: Biochemistry / Year: 2006
Title: Coiled Coils at the Edge of Configurational Heterogeneity. Structural Analyses of Parallel and Antiparallel Homotetrameric Coiled Coils Reveal Configurational Sensitivity to a Single Solvent- ...Title: Coiled Coils at the Edge of Configurational Heterogeneity. Structural Analyses of Parallel and Antiparallel Homotetrameric Coiled Coils Reveal Configurational Sensitivity to a Single Solvent-Exposed Amino Acid Substitution.
Authors: Yadav, M.K. / Leman, L.J. / Price, D.J. / Brooks, C.L. / Stout, C.D. / Ghadiri, M.R.
History
DepositionAug 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4
C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)17,1764
Polymers17,1764
Non-polymers00
Water19811
1
A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4

A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)17,1764
Polymers17,1764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
2
C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)17,1764
Polymers17,1764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.691, 37.192, 103.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein/peptide
GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / PLI KYHC


Mass: 4294.042 Da / Num. of mol.: 4 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 251 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: ...ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 251 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 256 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: CYS 268 TO GLU ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 275 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 276 TO LYS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39 %
Description: BEAM WAS INADVERTENTLY ALIGNED TO CU K BETA EDGE.
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: HANGING DROP, 1 UL OF 10 MG/ML PEPTIDE IN WATER TO 1UL OF 0.07M TRI-SODIUM CITRATE DIHYDRATE PH 5.6 0.7M AMMONIUM DIHYDROGEN PHOSPHATE %30 V/V GLYCEROL, HAMPTON CRYSTAL SCREEN CRYO NUMBER 11

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.3922
DetectorDate: Mar 19, 2003 / Details: CONFOCAL
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3922 Å / Relative weight: 1
ReflectionResolution: 2.2→52 Å / Num. obs: 7116 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.15 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 10.7 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→18.6 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.478 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 330 4.7 %RANDOM
Rwork0.228 ---
obs0.231 6718 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 0 11 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0211114
X-RAY DIFFRACTIONr_bond_other_d0.0080.021116
X-RAY DIFFRACTIONr_angle_refined_deg2.3492.0161479
X-RAY DIFFRACTIONr_angle_other_deg1.14732551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1455132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1770.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021215
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02239
X-RAY DIFFRACTIONr_nbd_refined0.2510.2260
X-RAY DIFFRACTIONr_nbd_other0.2780.21207
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0990.2677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4530.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6031.5672
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.51721071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2823442
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.8784.5408
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→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 27
Rwork0.188 460

+
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