[English] 日本語
Yorodumi
- PDB-1kb2: Crystal Structure of VDR DNA-binding Domain Bound to Mouse Osteop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kb2
TitleCrystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response Element
Components
  • 5'-D(*CP*AP*CP*GP*GP*TP*TP*CP*AP*CP*GP*AP*GP*GP*TP*TP*CP*A)-3'
  • 5'-D(*TP*GP*AP*AP*CP*CP*TP*CP*GP*TP*GP*AP*AP*CP*CP*GP*TP*G)-3'
  • Vitamin D3 Receptor
KeywordsTRANSCRIPTION/DNA / VDR / NUCLEAR RECEPTOR / PROTEIN-DNA COMPLEX / VITAMIN D / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


: / positive regulation of vitamin D 24-hydroxylase activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity ...: / positive regulation of vitamin D 24-hydroxylase activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / phosphate ion transmembrane transport / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / nuclear steroid receptor activity / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / intracellular receptor signaling pathway / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / intracellular calcium ion homeostasis / nuclear receptor activity / calcium ion transport / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Vitamin D receptor / VDR, DNA-binding domain / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Vitamin D receptor / VDR, DNA-binding domain / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShaffer, P.L. / Gewirth, D.T.
CitationJournal: EMBO J. / Year: 2002
Title: Structural basis of VDR-DNA interactions on direct repeat response elements.
Authors: Shaffer, P.L. / Gewirth, D.T.
History
DepositionNov 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*CP*AP*CP*GP*GP*TP*TP*CP*AP*CP*GP*AP*GP*GP*TP*TP*CP*A)-3'
D: 5'-D(*TP*GP*AP*AP*CP*CP*TP*CP*GP*TP*GP*AP*AP*CP*CP*GP*TP*G)-3'
A: Vitamin D3 Receptor
B: Vitamin D3 Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2018
Polymers36,9404
Non-polymers2624
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.14, 62.14, 241.75
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: DNA chain 5'-D(*CP*AP*CP*GP*GP*TP*TP*CP*AP*CP*GP*AP*GP*GP*TP*TP*CP*A)-3'


Mass: 5516.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MOUSE OSTEOPONTIN (SPP) RESPONSE ELEMENT
#2: DNA chain 5'-D(*TP*GP*AP*AP*CP*CP*TP*CP*GP*TP*GP*AP*AP*CP*CP*GP*TP*G)-3'


Mass: 5516.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MOUSE OSTEOPONTIN (SPP) RESPONSE ELEMENT
#3: Protein Vitamin D3 Receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor


Mass: 12953.305 Da / Num. of mol.: 2 / Fragment: DNA-binding Domain (Residues 16-125)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VDR / Plasmid: PET11A-VDR-N1-RPLKS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11473
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 8000, magnesium chloride, MES, glycerol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2MgCl211
3MES11
4glycerol11
5DTT11
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.33-0.66 mMprotein1drop
25 mMTris1droppH7.6
350 mM1dropNaCl
42 mMdithiothreitol1drop
54-6 %PEG40001reservoir
650 mMMES1reservoirpH5.6
75 mM1reservoirMgCl2
810 %glycerol1reservoir
910 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13744 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 60.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 22.9
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1342 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.76

-
Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KB4

1kb4


Resolution: 2.7→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 511147.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD FUNCTION
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1277 10.2 %RANDOM
Rwork0.226 ---
all-12490 --
obs-12490 90.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.0135 Å2 / ksol: 0.29281 e/Å3
Displacement parametersBiso mean: 72.3 Å2
Baniso -1Baniso -2Baniso -3
1-16.66 Å20 Å20 Å2
2--16.66 Å20 Å2
3----33.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 732 4 35 2135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d1.39
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.422
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.467 113 10.4 %
Rwork0.42 969 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PARAM_ZN
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 10433 / % reflection Rfree: 10 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0146
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.39
LS refinement shell
*PLUS
Rfactor Rfree: 0.467 / Rfactor Rwork: 0.42

+
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