[English] 日本語
Yorodumi
- PDB-3k7z: GCN4-Leucine zipper core mutant as N16A trigonal automatic solution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k7z
TitleGCN4-Leucine zipper core mutant as N16A trigonal automatic solution
ComponentsGeneral control protein GCN4
KeywordsDNA BINDING PROTEIN / COILED COIL / LEUCINE ZIPPER / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Activator / Amino-acid biosynthesis / DNA-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation
Function / homology
Function and homology information


protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsHolton, J. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Automated Protein Crystal Structure Determination Using Elves.
Authors: Holton, J. / Alber, T.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: An Engineered Allosteric Switch in Leucine-Zipper Oligomerization
Authors: Gonzalez Jr., L. / Plecs, J.J. / Alber, T.
#2: Journal: Nature / Year: 1994
Title: Crystal Structure of an Isoleucine-Zipper Trimer
Authors: Harbury, P.B. / Kim, P.S. / Alber, T.
#3: Journal: Science / Year: 1993
Title: A Switch between Two-, Three-, and Four-Stranded Coiled Coils in GCN4 Leucine Zipper Mutants
Authors: Harbury, P.B. / Zhang, T. / Kim, P.S. / Alber, T.
#4: Journal: Science / Year: 1991
Title: X-Ray Structure of the GCN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil.
Authors: O'Shea, E.K. / Klemm, J.D. / Kim, P.S. / Alber, T.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionNov 24, 2009ID: 1RB1
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
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


Theoretical massNumber of molelcules
Total (without water)11,8883
Polymers11,8883
Non-polymers00
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-37 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.943, 89.943, 46.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein/peptide General control protein GCN4 / Amino acid biosynthesis regulatory protein


Mass: 3962.639 Da / Num. of mol.: 3 / Fragment: LEUCINE-ZIPPER (RESIDUES 249-281) / Mutation: N16A / Source method: obtained synthetically
Details: THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE. THE PROTEIN WAS SYNTHESIZED BY SOLID PHASE PEPTIDE SYNTHESIS.
References: UniProt: P03069
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.54 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 100MM BIS-TRIS buffer only, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.0688, 0.9800, 0.9795, 0.9322
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 1997
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.06881
20.981
30.97951
40.93221
ReflectionResolution: 1.8→45 Å / Num. all: 23719 / Num. obs: 23195 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Rmerge(I) obs: 0.097
Reflection shellResolution: 1.8→1.9 Å / % possible all: 98.4

-
Processing

Software
NameVersionClassification
SSRLBL1-5data collection
ELVESmodel building
REFMAC4refinement
MOSFLMdata reduction
SCALAdata scaling
ELVESphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→25.96 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: refmac
Details: THIS ENTRY WAS SOLVED USING AUTOMATED STRUCTURE WHILE RELATED ENTRTY 1RB5 WAS SOLVED USING NON-AUTOMATED STRUCTURE DETERMINATION METHOD. THE NUMBER OF CLOSE CONTACTS IN THIS STRUCTURE IS AN ...Details: THIS ENTRY WAS SOLVED USING AUTOMATED STRUCTURE WHILE RELATED ENTRTY 1RB5 WAS SOLVED USING NON-AUTOMATED STRUCTURE DETERMINATION METHOD. THE NUMBER OF CLOSE CONTACTS IN THIS STRUCTURE IS AN ARTIFACT OF THE CURRENT STATE-OF-THE-ART AUTOMATED MODEL BUILDING PROCEDURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 861 5.2 %RANDOM
Rwork0.202 ---
all0.204 17020 --
obs0.204 16998 --
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms719 0 0 621 1340

+
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