[English] 日本語
Yorodumi
- PDB-3m48: GCN4 Leucine Zipper Peptide Mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m48
TitleGCN4 Leucine Zipper Peptide Mutant
ComponentsGeneral control protein GCN4
KeywordsDNA BINDING PROTEIN / GCN4 / leucine zipper / synthetic peptide / alpha helix / Activator / Amino-acid biosynthesis / DNA-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å
AuthorsDu, S. / Kettering, R.D. / Alvarado, J.J. / Tortajada, A. / Yeh, J.I.
CitationJournal: To be Published
Title: GCN4 Leucine Zipper Peptide Mutant
Authors: Du, S. / Kettering, R.D. / Alvarado, J.J. / Tortajada, A. / Yeh, J.I.
History
DepositionMar 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)3,9493
Polymers3,9031
Non-polymers462
Water36020
1
A: General control protein GCN4
hetero molecules

A: General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8976
Polymers7,8052
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1370 Å2
ΔGint-36 kcal/mol
Surface area5100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.275, 31.275, 57.507
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-16-

ASN

-
Components

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


Mass: 3902.543 Da / Num. of mol.: 1 / Fragment: Leucine Zipper domain (UNP residues 249-281) / Mutation: K251A, D255A, Y265W, H266N / Source method: obtained synthetically / Details: Synthetic peptide with the sequence of yeast GCN4 / References: UniProt: P03069
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 8 mg/ml leucine zipper peptide, 0.1M sodium acetate, 0.2M calcium chloride, 20% v/v 2-propanol, pH 4.6, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2005 / Details: Double silicon (111) crystal monochromator
RadiationMonochromator: double silicon (111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→25 Å / Num. obs: 5721 / % possible obs: 96.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 20.59 Å2 / Rsym value: 0.058 / Net I/σ(I): 32.3
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 399 / Rsym value: 0.342 / % possible all: 71.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I1G

3i1g


Resolution: 1.451→25 Å / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: MLHL / Details: TLS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 293 5.12 %random
Rwork0.2094 ---
obs0.2101 5721 93.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 101.186 Å2 / ksol: 0.507 e/Å3
Displacement parametersBiso mean: 20.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.9787 Å2-0 Å20 Å2
2---0.9787 Å2-0 Å2
3---1.9574 Å2
Refinement stepCycle: LAST / Resolution: 1.451→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms238 0 2 20 260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006306
X-RAY DIFFRACTIONf_angle_d0.917417
X-RAY DIFFRACTIONf_dihedral_angle_d15.325125
X-RAY DIFFRACTIONf_chiral_restr0.04546
X-RAY DIFFRACTIONf_plane_restr0.00257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4508-1.82770.27841380.20962490X-RAY DIFFRACTION87
1.8277-24.50670.21711550.20812938X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 2.3717 Å / Origin y: 6.6962 Å / Origin z: -4.8547 Å
111213212223313233
T0.2264 Å2-0.1029 Å20.0191 Å2-0.264 Å2-0.0011 Å2--0.1229 Å2
L1.9823 °21.43 °2-0.8787 °2-2.9598 °2-0.5976 °2--0.875 °2
S-0.1185 Å °0.5353 Å °-0.0672 Å °-0.028 Å °0.3478 Å °-0.0945 Å °-0.1279 Å °-0.1198 Å °-0.2008 Å °
Refinement TLS groupSelection details: all

+
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