[English] 日本語
Yorodumi
- PDB-5vpa: Transcription factor FosB/JunD bZIP domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vpa
TitleTranscription factor FosB/JunD bZIP domain
Components
  • Protein fosB
  • Transcription factor jun-D
KeywordsTRANSCRIPTION / activator protein-1 / basic leucine zipper / bZIP / fos / jun / transcription factor / DNA-binding protein / redox switch / coiled-coil
Function / homology
Function and homology information


transcription factor AP-1 complex / NGF-stimulated transcription / response to morphine / osteoblast development / response to corticosterone / behavioral response to cocaine / positive regulation of osteoblast differentiation / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP ...transcription factor AP-1 complex / NGF-stimulated transcription / response to morphine / osteoblast development / response to corticosterone / behavioral response to cocaine / positive regulation of osteoblast differentiation / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP / response to amphetamine / cellular response to calcium ion / transcription repressor complex / transcription coregulator binding / response to progesterone / female pregnancy / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / Estrogen-dependent gene expression / transcription regulator complex / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
AP-1 transcription factor / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper ...AP-1 transcription factor / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor JunD / Protein FosB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsYin, Z. / Machius, M. / Rudenko, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01 DA040621 United States
Brain and Behavior Research Foundation United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Activator Protein-1: redox switch controlling structure and DNA-binding.
Authors: Yin, Z. / Machius, M. / Nestler, E.J. / Rudenko, G.
History
DepositionMay 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein fosB
B: Transcription factor jun-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3154
Polymers16,2572
Non-polymers582
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-35 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.605, 95.352, 98.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Protein fosB / G0/G1 switch regulatory protein 3


Mass: 8267.290 Da / Num. of mol.: 1 / Fragment: unp residues 153-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOSB, G0S3 / Plasmid: pET21-NESG / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P53539
#2: Protein Transcription factor jun-D


Mass: 7989.425 Da / Num. of mol.: 1 / Fragment: unp residues 266-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JUND / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P17535
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.79 Å3/Da / Density % sol: 67.52 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3 M 1,6-Hexanediol, 50 mM Tris pH 8.5 and 5 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 13, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.83→34.204 Å / Num. obs: 6010 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 32.12 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.033 / Rrim(I) all: 0.102 / Χ2: 0.976 / Net I/σ(I): 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.83-2.859.51.1672.20.8260.391.2321.049100
2.85-2.99.41.0620.8550.3581.1221.006100
2.9-2.969.80.8630.9210.2840.911.003100
2.96-3.0210.20.8860.9350.2840.9311.056100
3.02-3.0810.10.7260.9510.2360.7641.024100
3.08-3.159.90.8530.9230.2810.8991.001100
3.15-3.239.80.5410.9750.1770.570.976100
3.23-3.329.30.4490.9730.1510.4740.933100
3.32-3.428.90.3560.980.1230.3771.012100
3.42-3.539.30.2730.9930.0920.2890.989100
3.53-3.659.50.190.9920.0640.2011.049100
3.65-3.810.10.1450.9920.0480.1530.976100
3.8-3.979.80.0980.9980.0320.1030.934100
3.97-4.189.80.0850.9980.0270.0890.957100
4.18-4.4490.0730.9980.0250.0770.996100
4.44-4.799.10.060.9990.020.0630.921100
4.79-5.2710.20.0570.9990.0190.060.907100
5.27-6.039.60.0750.9980.0250.0790.825100
6.03-7.598.60.0530.9990.0180.0570.894100
7.59-34.2048.70.0610.9920.0220.0651.00999.7

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FOS

1fos


Resolution: 2.83→34.204 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.57
RfactorNum. reflection% reflection
Rfree0.2828 433 9.8 %
Rwork0.2446 --
obs0.2484 4417 71.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 185.72 Å2 / Biso mean: 66.4615 Å2 / Biso min: 4.48 Å2
Refinement stepCycle: final / Resolution: 2.83→34.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 2 5 886
Biso mean--46.79 14.68 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006903
X-RAY DIFFRACTIONf_angle_d0.6851209
X-RAY DIFFRACTIONf_chiral_restr0.029144
X-RAY DIFFRACTIONf_plane_restr0.003158
X-RAY DIFFRACTIONf_dihedral_angle_d13.159599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8297-3.23890.3372760.271569977539
3.2389-4.07960.27841450.24931374151974
4.0796-34.20690.27462120.235919112123100
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)
11.80591.2732-0.64824.44980.85791.80380.52910.0036-0.83530.43380.16410.07690.8482-0.369-0.52230.3855-0.1781-0.09610.377-0.07370.78893.95419.4427285.432
22.7939-1.8837-2.63944.74934.46826.6989-0.09060.1695-0.11820.2003-0.07470.3608-0.0351-0.29750.21930.09250.0763-0.07690.4611-0.10440.123-2.121827.1751317.0291
31.1253-0.3911-1.45631.02851.122.6817-0.08070.1284-0.0127-0.10530.0882-0.0019-0.11310.1051-0.24180.0746-0.05660.09410.4294-0.0305-0.05686.769124.593308.7369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 177 )A164 - 177
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 217 )A178 - 217
3X-RAY DIFFRACTION3chain 'B' and (resid 275 through 332 )B275 - 332

+
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