[English] 日本語
Yorodumi
- PDB-7xi3: Crystal Structure of the NPAS4-ARNT2 heterodimer in complex with DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xi3
TitleCrystal Structure of the NPAS4-ARNT2 heterodimer in complex with DNA
Components
  • Aryl hydrocarbon receptor nuclear translocator 2
  • DNA (5'-D(P*CP*CP*AP*TP*CP*AP*CP*TP*CP*AP*CP*GP*AP*CP*CP*T)-3')
  • DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*TP*GP*AP*T)-3')
  • Neuronal PAS domain protein 4
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


protein dimerization activity / regulation of DNA-templated transcription / nucleus
Similarity search - Function
PAS fold-3 / PAS fold / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Neuronal PAS domain protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.274 Å
AuthorsSun, X.N. / Jing, L.Q. / Li, F.W. / Wu, D.L.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentZR2021JQ30 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers reveal new dimerization modalities in the bHLH-PAS transcription factor family.
Authors: Sun, X. / Jing, L. / Li, F. / Zhang, M. / Diao, X. / Zhuang, J. / Rastinejad, F. / Wu, D.
History
DepositionApr 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: 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 29, 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: Aryl hydrocarbon receptor nuclear translocator 2
B: Neuronal PAS domain protein 4
C: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*TP*GP*AP*T)-3')
D: DNA (5'-D(P*CP*CP*AP*TP*CP*AP*CP*TP*CP*AP*CP*GP*AP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)92,3234
Polymers92,3234
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-82 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.773, 72.773, 415.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator 2


Mass: 44215.363 Da / Num. of mol.: 1 / Fragment: ARNT2
Source method: isolated from a genetically manipulated source
Details: AUTHORS STATE THAT THE NCBI ACCESSION NUMBER IS OK136250 FOR THIS POLYMER.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt2 / Plasmid: pMKH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Protein Neuronal PAS domain protein 4


Mass: 38310.688 Da / Num. of mol.: 1 / Fragment: NPAS4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Npas4 / Plasmid: pSJ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A1L327
#3: DNA chain DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*TP*GP*AP*T)-3')


Mass: 5034.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(P*CP*CP*AP*TP*CP*AP*CP*TP*CP*AP*CP*GP*AP*CP*CP*T)-3')


Mass: 4763.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.69 % / Mosaicity: 0.706 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8 / Details: sodium citrate tribasic, PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: SIEMENS-NICOLET / Detector: PIXEL / Date: Jul 18, 2021 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 4.274→50 Å / Num. obs: 8463 / % possible obs: 99 % / Redundancy: 9.3 % / Biso Wilson estimate: 46.27 Å2 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.062 / Rrim(I) all: 0.192 / Χ2: 0.853 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.3-4.375.90.6793800.8230.2770.7370.86895
4.37-4.456.40.6443860.8320.2590.6970.82396.3
4.45-4.546.40.6154080.9030.2420.6640.87198.3
4.54-4.6370.6114050.8580.2350.6580.94799.5
4.63-4.737.60.4944120.9490.180.5280.92398.6
4.73-4.848.50.5044030.9410.1750.5350.92599.5
4.84-4.968.60.4944230.9450.1740.5250.913100
4.96-5.19.50.4734000.9380.1570.50.911100
5.1-5.2510.20.5074320.9680.1640.5330.86599.3
5.25-5.42110.5044020.9660.1560.5290.793100
5.42-5.6111.30.4354260.9770.1340.4560.838100
5.61-5.8310.60.3854160.9710.1230.4050.83899.8
5.83-6.1120.3794410.9760.1140.3960.79799.5
6.1-6.4211.40.3174020.9780.0960.3310.78399.5
6.42-6.8212.40.2724400.9860.0790.2830.769100
6.82-7.3512.20.1874420.9920.0550.1950.811100
7.35-8.0811.60.1344300.9950.0410.140.865100
8.08-9.259.60.0984490.990.0330.1041.03299.6
9.25-11.636.90.0654500.9950.0260.070.9297.4
11.63-506.70.0545160.9940.0240.0590.69297.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPK

4zpk


Resolution: 4.274→15.969 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3146 384 5.03 %
Rwork0.2489 7255 -
obs0.2523 7639 92.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.84 Å2 / Biso mean: 50.1771 Å2 / Biso min: 22.04 Å2
Refinement stepCycle: final / Resolution: 4.274→15.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 656 0 0 5436
Num. residues----633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.274-4.87640.3045980.2655198078
4.8764-6.08670.3451530.28152557100
6.0867-15.9690.29271330.2129271899

+
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