3BRD

CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, P212121

> Summary

Summary for 3BRD

Related3BRF 3BRG
DescriptorLin-12 and glp-1 phenotype protein 1, isoform a, Protein lin-12/DNA Complex
Functional Keywordsprotein-dna complex, signaling, transcription, notch, dna-binding, ank repeat, developmental protein, differentiation, egf-like domain, glycoprotein, membrane, transmembrane, dna binding protein-dna complex, dna binding protein/dna
Biological sourceCaenorhabditis elegans
Cellular locationMembrane; Single-pass type I membrane protein P14585
Total number of polymer chains4
Total molecular weight67082.14
Authors
Wilson, J.J.,Kovall, R.A. (deposition date: 2007-12-21, release date: 2008-04-01, modification date: 2009-02-24)
Primary citation
Friedmann, D.R.,Wilson, J.J.,Kovall, R.A.
RAM-induced Allostery Facilitates Assembly of a Notch Pathway Active Transcription Complex.
J.Biol.Chem., 283:14781-14791, 2008
PubMed: 18381292
DOI: 10.1074/jbc.M709501200
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.21 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.27870.7%9.2%18.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3brd
no rotation
Molmil generated image of 3brd
rotated about x axis by 90°
Molmil generated image of 3brd
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
BDNA (5'-D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3')polymer154673.11
CDNA (5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3')polymer154504.01
ALin-12 and glp-1 phenotype protein 1, isoform apolymer47753762.31
UniProt (Q9TYY1)
Pfam (PF09270)
Pfam (PF09271)
UniProt (by SIFTS) (Q8MXE7)
Caenorhabditis elegans@PDBjDNA-binding protein LAG-1, Lag-1 protein
DProtein lin-12polymer293522.11
UniProt (P14585)
Caenorhabditis elegans@PDBjAbnormal cell lineage protein 12
1,2-ETHANEDIOLnon-polymer62.110
waterwater18.0131

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight66461.5
Non-Polymers*Number of molecules10
Total molecular weight620.7
All*Total molecular weight67082.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.21 Å)

Cell axes60.15398.866126.313
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits39.87 - 2.21
the highest resolution shell value2.264 - 2.210
R-factor0.211
R-work0.20800
the highest resolution shell value0.267
R-free0.25700
the highest resolution shell value0.307
RMSD bond length0.018
RMSD bond angle1.795

Data Collection Statistics

Resolution limits50.00 - 2.20
the highest resolution shell value -
Number of reflections36557
Rmerge_l_obs0.066
the highest resolution shell value0.345
Completeness94.8
Redundancy5.5
the highest resolution shell value5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1under oil microbatch5.5277
1under oil microbatch5.5277
1under oil microbatch5.5277
1under oil microbatch5.5277
1under oil microbatch5.5277
1under oil microbatch5.5277
1under oil microbatch5.5277
1under oil microbatch5.5277
1under oil microbatch5.5277
1under oil microbatch5.5277

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
111Bis
211Tris
311Ammonium Sulfate
411PEG 3350
511Ethylene Glycol
612Bis
712Tris
812Ammonium Sulfate
912PEG 3350
1012Ethylene Glycol
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
D0016324cellular_componentapical plasma membrane
D0016021cellular_componentintegral component of membrane
D0005634cellular_componentnucleus
D0005886cellular_componentplasma membrane
D0005509molecular_functioncalcium ion binding
D0004888molecular_functiontransmembrane signaling receptor activity
D0001708biological_processcell fate specification
D0045168biological_processcell-cell signaling involved in cell fate commitment
D0043054biological_processdauer exit
D0002119biological_processnematode larval development
D0007219biological_processNotch signaling pathway
D0018991biological_processoviposition
D0040025biological_processvulval development
A0005634cellular_componentnucleus
A0005112molecular_functionNotch binding
A0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
A0043565molecular_functionsequence-specific DNA binding
A0000982molecular_functiontranscription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding
A0001708biological_processcell fate specification
A0043054biological_processdauer exit
A0042078biological_processgerm-line stem cell division
A0002119biological_processnematode larval development
A0007219biological_processNotch signaling pathway
A0018991biological_processoviposition
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0040026biological_processpositive regulation of vulval development
A0042659biological_processregulation of cell fate specification
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC17BINDING SITE FOR RESIDUE EDO A 1
ChainResidue
APHE34
ACYS55
ATYR57
ATRP236
AALA238
AHOH
AHOH

AC23BINDING SITE FOR RESIDUE EDO A 2
ChainResidue
ATHR443
AASN444
AARG445

AC34BINDING SITE FOR RESIDUE EDO A 3
ChainResidue
AGLU359
AARG361
ASER465
AGLY467

AC44BINDING SITE FOR RESIDUE EDO A 4
ChainResidue
AGLN175
ALYS357
AALA358
AGLU359

AC56BINDING SITE FOR RESIDUE EDO A 5
ChainResidue
AGLN114
AGLN115
AALA140
AALA141
ALYS142
ATHR143

AC65BINDING SITE FOR RESIDUE EDO D 6
ChainResidue
ATHR276
AGLY277
AILE278
DALA14
DSER15

AC71BINDING SITE FOR RESIDUE EDO C 16
ChainResidue
CDT6

AC82BINDING SITE FOR RESIDUE EDO A 8
ChainResidue
ATYR103
APHE162

AC94BINDING SITE FOR RESIDUE EDO A 9
ChainResidue
ALEU21
AMET441
APHE442
APRO453

BC15BINDING SITE FOR RESIDUE EDO A 10
ChainResidue
AARG259
APHE262
AGLU394
AARG418
AHOH

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
EDO_3brd_C_1691,2-ETHANEDIOL binding site
ChainResidueligand
CDT6-DT7EDO: 1,2-ETHANEDIOL
ALYS227EDO: 1,2-ETHANEDIOL
ALYS337-LYS339EDO: 1,2-ETHANEDIOL
AVAL365-SER367EDO: 1,2-ETHANEDIOL

EDO_3brd_A_961,2-ETHANEDIOL binding site
ChainResidueligand
ALEU207EDO: 1,2-ETHANEDIOL
ALYS210EDO: 1,2-ETHANEDIOL
AMET627-PHE628EDO: 1,2-ETHANEDIOL
AGLU637EDO: 1,2-ETHANEDIOL
APRO639EDO: 1,2-ETHANEDIOL

EDO_3brd_A_181,2-ETHANEDIOL binding site
ChainResidueligand
APHE220EDO: 1,2-ETHANEDIOL
ACYS241EDO: 1,2-ETHANEDIOL
ATYR243EDO: 1,2-ETHANEDIOL
ATRP422-ALA424EDO: 1,2-ETHANEDIOL
ASER460-VAL461EDO: 1,2-ETHANEDIOL

EDO_3brd_A_851,2-ETHANEDIOL binding site
ChainResidueligand
AVAL287EDO: 1,2-ETHANEDIOL
ATYR289EDO: 1,2-ETHANEDIOL
APHE348-TYR349EDO: 1,2-ETHANEDIOL
AGLY352EDO: 1,2-ETHANEDIOL

EDO_3brd_A_591,2-ETHANEDIOL binding site
ChainResidueligand
AGLN300-ASP303EDO: 1,2-ETHANEDIOL
AALA326-LEU330EDO: 1,2-ETHANEDIOL

EDO_3brd_A_471,2-ETHANEDIOL binding site
ChainResidueligand
AGLN361EDO: 1,2-ETHANEDIOL
ALYS543-TYR546EDO: 1,2-ETHANEDIOL
AVAL564EDO: 1,2-ETHANEDIOL
AARG584EDO: 1,2-ETHANEDIOL

EDO_3brd_A_1071,2-ETHANEDIOL binding site
ChainResidueligand
ALEU429EDO: 1,2-ETHANEDIOL
AARG445EDO: 1,2-ETHANEDIOL
AGLY447-TYR450EDO: 1,2-ETHANEDIOL
ASER453EDO: 1,2-ETHANEDIOL

EDO_3brd_D_661,2-ETHANEDIOL binding site
ChainResidueligand
ATHR462-ILE464EDO: 1,2-ETHANEDIOL
DASN941-SER943EDO: 1,2-ETHANEDIOL

EDO_3brd_A_361,2-ETHANEDIOL binding site
ChainResidueligand
AGLU545-ARG547EDO: 1,2-ETHANEDIOL
ASER651-GLY653EDO: 1,2-ETHANEDIOL

EDO_3brd_A_271,2-ETHANEDIOL binding site
ChainResidueligand
AMET627-THR632EDO: 1,2-ETHANEDIOL
AGLU637EDO: 1,2-ETHANEDIOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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