[English] 日本語
Yorodumi
- PDB-6iak: The crystal structure of the chicken CREB3 bZIP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iak
TitleThe crystal structure of the chicken CREB3 bZIP
ComponentsUncharacterized protein
KeywordsTRANSCRIPTION / CREB3 / bZIP / crystallographic structure / homodimeric bZIP unbound to DNA.
Function / homology
Function and homology information


: / CREB3 factors activate genes / cAMP response element binding / positive regulation of monocyte chemotaxis / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / endoplasmic reticulum ...: / CREB3 factors activate genes / cAMP response element binding / positive regulation of monocyte chemotaxis / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleus / cytosol
Similarity search - Function
cAMP-responsive element-binding protein 3 / bZIP transcription factor / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BZIP domain-containing protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.95 Å
AuthorsSabaratnam, K. / Renner, M.
CitationJournal: Protein Sci. / Year: 2019
Title: Insights from the crystal structure of the chicken CREB3 bZIP suggest that members of the CREB3 subfamily transcription factors may be activated in response to oxidative stress.
Authors: Sabaratnam, K. / Renner, M. / Paesen, G. / Harlos, K. / Nair, V. / Owens, R.J. / Grimes, J.M.
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)341,5467
Polymers341,5467
Non-polymers00
Water00
1
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)97,5852
Polymers97,5852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-20 kcal/mol
Surface area11320 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)97,5852
Polymers97,5852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-20 kcal/mol
Surface area10450 Å2
MethodPISA
3
E: Uncharacterized protein
F: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)97,5852
Polymers97,5852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-20 kcal/mol
Surface area11860 Å2
MethodPISA
4
G: Uncharacterized protein

G: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)97,5852
Polymers97,5852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z1
Buried area1200 Å2
ΔGint-14 kcal/mol
Surface area6730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.900, 167.060, 115.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

-
Components

#1: Protein
Uncharacterized protein


Mass: 48792.289 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CREB3 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) pLysS / References: UniProt: F1P542
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity % sol: 85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 50% v/v 2-Methyl-2,4- pentanediol (MPD), 100mM Tri-sodium citrate pH 5.6, 10mM Magnesium chloride (MORPHEUS screen)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.95→51.64 Å / Num. obs: 12046 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 114.77 Å2 / CC1/2: 0.93 / Rmerge(I) obs: 0.3 / Net I/σ(I): 3.3
Reflection shellResolution: 3.95→4.09 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1 / Num. unique obs: 887 / CC1/2: 0.76 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.95→51.64 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.631
RfactorNum. reflection% reflectionSelection details
Rfree0.3 605 5.03 %RANDOM
Rwork0.261 ---
obs0.263 12028 99.8 %-
Displacement parametersBiso mean: 158.71 Å2
Baniso -1Baniso -2Baniso -3
1--4.214 Å20 Å20 Å2
2---5.6372 Å20 Å2
3---9.8513 Å2
Refine analyzeLuzzati coordinate error obs: 0.7 Å
Refinement stepCycle: 1 / Resolution: 3.95→51.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 0 0 3563
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0153574HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.674729HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1512SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes611HARMONIC5
X-RAY DIFFRACTIONt_it3574HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion27.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion442SEMIHARMONIC5
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_contact4296SEMIHARMONIC4
LS refinement shellResolution: 3.95→4 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.3977 -3.49 %
Rwork0.2946 387 -
all0.2985 401 -
obs--99.01 %
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)
13.9044-5.82081.97848.2001-2.02392.822-0.2387-0.1649-0.2562-0.00020.357-0.1762-0.2391-0.2896-0.11840.60790.16090.03430.2051-0.0936-0.4434142.829193.21929.5424
21.9604-5.6002-1.294816.00233.54342.42370.2025-0.0077-0.0131-0.90020.1252-0.5238-0.26740.4771-0.32770.01620.20940.00090.29380.1454-0.5712146.87188.89435.086
35.92853.6812-3.78670-0.64411.829-0.39550.81880.6992-0.46820.44030.1716-1.0616-0.2851-0.04480.60790.2971-0.28310.46830.1258-0.6079126.373200.40813.6385
415.52592.5463.507800.6624.5088-0.0003-0.3671-0.1101-0.4836-0.17220.26610.27010.36720.17250.44750.22160.125-0.3733-0.0243-0.4996129.315197.74120.1343
59.49095.1464-0.5672.97361.00810.7102-0.12120.50660.5595-0.37640.16940.0083-0.29570.1368-0.04820.3744-0.1149-0.0120.1874-0.0242-0.5607144.62206.58753.8182
67.08315.82081.81087.37432.56691.71340.29530.68280.38310.20260.1171-0.4278-0.40450.6499-0.41240.49740.07810.15250.39010.1818-0.4867141.627206.65645.0905
72.28420.63640.185612.05692.337816.63090.0178-0.0953-0.2374-0.75820.12410.83-1.0885-1.0885-0.14180.60790.3040.06520.10540.0084-0.6079135.033201.7475.18
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }

+
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