[English] 日本語
Yorodumi
- PDB-2wpy: GCN4 leucine zipper mutant with one VxxNxxx motif coordinating ch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wpy
TitleGCN4 leucine zipper mutant with one VxxNxxx motif coordinating chloride
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsTRANSCRIPTION / AMINO-ACID BIOSYNTHESIS / TRANSCRIPTION REGULATION / ION COORDINATION / POLAR CORE RESIDUES / PROTEIN EXPORT / PHOSPHOPROTEIN / TAA / NUCLEUS / ACTIVATOR / DNA-BINDING / TRIMERIC AUTOTRANSPORTER ADHESIN
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / 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 / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZeth, K. / Hartmann, M.D. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A Coiled-Coil Motif that Sequesters Ions to the Hydrophobic Core.
Authors: Hartmann, M.D. / Ridderbusch, O. / Zeth, K. / Albrecht, R. / Testa, O. / Woolfson, D.N. / Sauer, G. / Dunin-Horkawicz, S. / Lupas, A.N. / Alvarez, B.H.
History
DepositionAug 12, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: GENERAL CONTROL PROTEIN GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0893
Polymers4,0181
Non-polymers712
Water34219
1
A: GENERAL CONTROL PROTEIN GCN4
hetero molecules

A: GENERAL CONTROL PROTEIN GCN4
hetero molecules

A: GENERAL CONTROL PROTEIN GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2669
Polymers12,0533
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4590 Å2
ΔGint-59.37 kcal/mol
Surface area6100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.330, 33.330, 50.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1033-

CL

21A-1034-

CL

-
Components

#1: Protein/peptide GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / GCN4 LEUCINE ZIPPER MUTANT


Mass: 4017.674 Da / Num. of mol.: 1 / Fragment: COILED-COIL DOMAIN, RESIDUES 249-281 / Mutation: YES / Source method: obtained synthetically / Details: N-TERMINAL ACETYL GROUP / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 264 TO VAL ENGINEERED RESIDUE IN CHAIN A, LEU 267 TO ASN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growDetails: 3.2 M NACL, 100 MM NA-ACETATE, PH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 3548 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.37 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 1.75→14.61 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.288 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25239 248 7 %RANDOM
Rwork0.21398 ---
obs0.21679 3292 100 %-
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: 44.815 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.77 Å20 Å2
2--1.55 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 1.75→14.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms267 0 2 19 288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022270
X-RAY DIFFRACTIONr_bond_other_d0.0370.02196
X-RAY DIFFRACTIONr_angle_refined_deg1.6032.013358
X-RAY DIFFRACTIONr_angle_other_deg1.4143483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.362531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10725.38513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5091563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.929152
X-RAY DIFFRACTIONr_chiral_restr0.0850.241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0245
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3646162
X-RAY DIFFRACTIONr_mcbond_other2.967665
X-RAY DIFFRACTIONr_mcangle_it5.6619260
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.65612108
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.6391898
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 18 -
Rwork0.328 231 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -11.571 Å / Origin y: 9.881 Å / Origin z: -4.482 Å
111213212223313233
T0.0249 Å2-0.01 Å20.0064 Å2-0.0532 Å2-0.0142 Å2--0.0385 Å2
L0.1005 °20.234 °2-0.1576 °2-0.7316 °2-1.1794 °2--6.2636 °2
S0.0077 Å °0.0405 Å °-0.0375 Å °0.0333 Å °0.0397 Å °-0.0466 Å °-0.0736 Å °0.1782 Å °-0.0474 Å °

+
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://pdbjlvh1.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