4G83

Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element

> Summary

Summary for 4G83

Related3vd0 3vd1 3vd2 4G82
DescriptorPROTEIN/DNA Complex
Functional Keywordsbeta-immunoglobulin fold, tumor suppressor, dna binding protein-dna complex, dna binding protein/dna
Biological sourceHomo sapiens (human)
More
Cellular locationNucleus O15350
Total number of polymer chains4
Total molecular weight59953.04
Authors
Ethayathulla, A.S.,Viadiu, H. (deposition date: 2012-07-20, release date: 2013-01-16, modification date: 2013-02-20)
Primary citation
Ethayathulla, A.S.,Viadiu, H.
Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element
J.Biol.Chem., 2013
Experimental method
X-RAY DIFFRACTION (4 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.328390.8%4.9%0MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4g83
no rotation
Molmil generated image of 4g83
rotated about x axis by 90°
Molmil generated image of 4g83
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 4g83
no rotation
Molmil generated image of 4g83
rotated about x axis by 90°
Molmil generated image of 4g83
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (4g83.pdb1.gz [303.92 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
E, Fdnapolymer206135.02
A, BTumor protein p73polymer21023776.12
UniProt (O15350)
Pfam (PF00870)
Homo sapiens (human)@PDBjp53-like transcription factor, p53-related protein
ZINC IONnon-polymer65.42

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight59822.3
Non-Polymers*Number of molecules2
Total molecular weight130.8
All*Total molecular weight59953.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (4 Å)

Cell axes141.71796.34534.348
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits45.61 - 4.00
the highest resolution shell value45.613 - 4.000
R-factor0.2443
R-work0.24140
the highest resolution shell value0.241
R-free0.30730
the highest resolution shell value0.307
RMSD bond length0.031
RMSD bond angle3.062

Data Collection Statistics

Resolution limits50.00 - 4.00
the highest resolution shell value -
Number of reflections5072
Rmerge_l_obs0.140
Completeness99.8
Redundancy7.6
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.5298

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
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
A0030054cellular_componentcell junction
A0000785cellular_componentchromatin
A0005829cellular_componentcytosol
A0005794cellular_componentGolgi apparatus
A0043231cellular_componentintracellular membrane-bounded organelle
A0005739cellular_componentmitochondrion
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0005667cellular_componenttranscription factor complex
A0003682molecular_functionchromatin binding
A0003684molecular_functiondamaged DNA binding
A0042802molecular_functionidentical protein binding
A0046872molecular_functionmetal ion binding
A0002039molecular_functionp53 binding
A0019901molecular_functionprotein kinase binding
A0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
A0000981molecular_functionRNA polymerase II transcription factor activity, sequence-specific DNA binding
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0008134molecular_functiontranscription factor binding
A0044212molecular_functiontranscription regulatory region DNA binding
A0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
A0000187biological_processactivation of MAPK activity
A0007050biological_processcell cycle arrest
A0006974biological_processcellular response to DNA damage stimulus
A0034644biological_processcellular response to UV
A0006978biological_processDNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
A0008630biological_processintrinsic apoptotic signaling pathway in response to DNA damage
A0042771biological_processintrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
A0001822biological_processkidney development
A0006298biological_processmismatch repair
A0031571biological_processmitotic G1 DNA damage checkpoint
A0060044biological_processnegative regulation of cardiac muscle cell proliferation
A0008285biological_processnegative regulation of cell proliferation
A0043508biological_processnegative regulation of JUN kinase activity
A0043524biological_processnegative regulation of neuron apoptotic process
A0045665biological_processnegative regulation of neuron differentiation
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0071158biological_processpositive regulation of cell cycle arrest
A0048714biological_processpositive regulation of oligodendrocyte differentiation
A1900740biological_processpositive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0045893biological_processpositive regulation of transcription, DNA-templated
A0051262biological_processprotein tetramerization
A0042981biological_processregulation of apoptotic process
A0010468biological_processregulation of gene expression
A0007346biological_processregulation of mitotic cell cycle
A1901796biological_processregulation of signal transduction by p53 class mediator
A0042493biological_processresponse to drug
A0010332biological_processresponse to gamma radiation
A0010243biological_processresponse to organonitrogen compound
A0010165biological_processresponse to X-ray
A0016032biological_processviral process
B0030054cellular_componentcell junction
B0000785cellular_componentchromatin
B0005829cellular_componentcytosol
B0005794cellular_componentGolgi apparatus
B0043231cellular_componentintracellular membrane-bounded organelle
B0005739cellular_componentmitochondrion
B0005654cellular_componentnucleoplasm
B0005634cellular_componentnucleus
B0005667cellular_componenttranscription factor complex
B0003682molecular_functionchromatin binding
B0003684molecular_functiondamaged DNA binding
B0042802molecular_functionidentical protein binding
B0046872molecular_functionmetal ion binding
B0002039molecular_functionp53 binding
B0019901molecular_functionprotein kinase binding
B0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
B0000981molecular_functionRNA polymerase II transcription factor activity, sequence-specific DNA binding
B0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
B0008134molecular_functiontranscription factor binding
B0044212molecular_functiontranscription regulatory region DNA binding
B0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
B0000187biological_processactivation of MAPK activity
B0007050biological_processcell cycle arrest
B0006974biological_processcellular response to DNA damage stimulus
B0034644biological_processcellular response to UV
B0006978biological_processDNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
B0008630biological_processintrinsic apoptotic signaling pathway in response to DNA damage
B0042771biological_processintrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
B0001822biological_processkidney development
B0006298biological_processmismatch repair
B0031571biological_processmitotic G1 DNA damage checkpoint
B0060044biological_processnegative regulation of cardiac muscle cell proliferation
B0008285biological_processnegative regulation of cell proliferation
B0043508biological_processnegative regulation of JUN kinase activity
B0043524biological_processnegative regulation of neuron apoptotic process
B0045665biological_processnegative regulation of neuron differentiation
B0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
B0071158biological_processpositive regulation of cell cycle arrest
B0048714biological_processpositive regulation of oligodendrocyte differentiation
B1900740biological_processpositive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway
B0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
B0045893biological_processpositive regulation of transcription, DNA-templated
B0051262biological_processprotein tetramerization
B0042981biological_processregulation of apoptotic process
B0010468biological_processregulation of gene expression
B0007346biological_processregulation of mitotic cell cycle
B1901796biological_processregulation of signal transduction by p53 class mediator
B0042493biological_processresponse to drug
B0010332biological_processresponse to gamma radiation
B0010243biological_processresponse to organonitrogen compound
B0010165biological_processresponse to X-ray
B0016032biological_processviral process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE ZN A 401
ChainResidue
ACYS194
AHIS197
ACYS258
ACYS262

AC24BINDING SITE FOR RESIDUE ZN B 401
ChainResidue
BCYS194
BHIS197
BCYS258
BCYS262

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

site_idNumber of ResiduesDetails
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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

> Sequence Neighbor

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