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- PDB-3qym: Structure of p63 DNA Binding Domain in Complex with a 10 Base Pai... -

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Basic information

Entry
Database: PDB / ID: 3qym
TitleStructure of p63 DNA Binding Domain in Complex with a 10 Base Pair A/T Rich Response Element Half Site
Components
  • 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
  • Tumor protein 63
KeywordsTRANSCRIPTION ACTIVATOR/DNA / B DNA double helix / protein-DNA complex / zinc binding / beta sandwich / greek key / transcription factor / DNA binding / nucleus / TRANSCRIPTION ACTIVATOR-DNA complex
Function / homology
Function and homology information


positive regulation of somatic stem cell population maintenance / positive regulation of fibroblast apoptotic process / negative regulation of intracellular estrogen receptor signaling pathway / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / positive regulation of cell cycle G1/S phase transition / Developmental Lineage of Mammary Stem Cells / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors ...positive regulation of somatic stem cell population maintenance / positive regulation of fibroblast apoptotic process / negative regulation of intracellular estrogen receptor signaling pathway / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / positive regulation of cell cycle G1/S phase transition / Developmental Lineage of Mammary Stem Cells / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / WW domain binding / positive regulation of Notch signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / regulation of epidermal cell division / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of cellular senescence / Developmental Lineage of Mammary Gland Myoepithelial Cells / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / establishment of skin barrier / positive regulation of osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / Notch signaling pathway / MDM2/MDM4 family protein binding / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein tetramerization / promoter-specific chromatin binding / p53 binding / regulation of apoptotic process / spermatogenesis / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / apoptotic process / positive regulation of cell population proliferation / DNA damage response / dendrite / positive regulation of DNA-templated transcription / chromatin / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Tumour protein p63, SAM domain / Immunoglobulin-like - #720 / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily ...Tumour protein p63, SAM domain / Immunoglobulin-like - #720 / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / Tumor protein 63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHerzberg, O. / Chen, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements.
Authors: Chen, C. / Gorlatova, N. / Kelman, Z. / Herzberg, O.
History
DepositionMar 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor protein 63
B: Tumor protein 63
C: Tumor protein 63
D: Tumor protein 63
E: Tumor protein 63
F: Tumor protein 63
G: Tumor protein 63
H: Tumor protein 63
I: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
J: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
K: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
L: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
M: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
N: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
O: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
P: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,33824
Polymers205,81516
Non-polymers5238
Water00
1
A: Tumor protein 63
B: Tumor protein 63
C: Tumor protein 63
D: Tumor protein 63
I: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
J: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
K: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
L: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,16912
Polymers102,9088
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Tumor protein 63
F: Tumor protein 63
G: Tumor protein 63
H: Tumor protein 63
M: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
N: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
O: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
P: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,16912
Polymers102,9088
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tumor protein 63
D: Tumor protein 63
E: Tumor protein 63
F: Tumor protein 63
K: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
L: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
M: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
N: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,16912
Polymers102,9088
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.872, 180.198, 104.379
Angle α, β, γ (deg.)90.00, 92.62, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is formed by a full response element, which binds two protein dimers. Protein dimer-dimer interaction is possible only if the two half sites are contiguous, and the relative orientation between the two protein dimers may vary. It is unknown which of the two arrangements of p63 dimers (BIOMOLECULE 1 and 2 versus BIOMOLECULE 3) is biologically relevant.

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Components

#1: Protein
Tumor protein 63 / p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / ...p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / Transformation-related protein 63 / TP63 / Tumor protein p73-like / p73L / p40 / p51


Mass: 22683.861 Da / Num. of mol.: 8 / Fragment: DNA binding domain (UNP residues 166-362)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KET, P63, P73H, P73L, TP63, TP73L / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9H3D4
#2: DNA chain
5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'


Mass: 3043.029 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: contains a consensus P63 binding motif
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 10% PEG3350, 0.2 M ammonium formate, 0.1 M Bis-Tris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9198
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 3.2→104.257 Å / Num. all: 36604 / Num. obs: 36604 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 85.29 Å2 / Rsym value: 0.14 / Net I/σ(I): 5.8
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2610 / Rsym value: 0.433 / % possible all: 94.5

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ADY

2ady


Resolution: 3.2→19.719 Å / SU ML: 0.52 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 31.77 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 1836 5.02 %RANDOM
Rwork0.245 ---
obs0.2463 36593 97.53 %-
all-36604 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.093 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.6736 Å20 Å210.4226 Å2
2---11.2551 Å20 Å2
3---1.5815 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12057 1616 8 0 13681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814148
X-RAY DIFFRACTIONf_angle_d1.37219545
X-RAY DIFFRACTIONf_dihedral_angle_d21.4275465
X-RAY DIFFRACTIONf_chiral_restr0.0952168
X-RAY DIFFRACTIONf_plane_restr0.012298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.28610.34921370.38362560X-RAY DIFFRACTION94
3.2861-3.38240.3991520.37422624X-RAY DIFFRACTION96
3.3824-3.4910.3721320.36372619X-RAY DIFFRACTION96
3.491-3.6150.39251300.35282674X-RAY DIFFRACTION97
3.615-3.75880.38471550.33842667X-RAY DIFFRACTION97
3.7588-3.92860.36311150.32162698X-RAY DIFFRACTION98
3.9286-4.13390.321310.28932683X-RAY DIFFRACTION98
4.1339-4.39020.28291560.25022688X-RAY DIFFRACTION98
4.3902-4.72490.27321430.22572680X-RAY DIFFRACTION99
4.7249-5.19250.22751300.18652709X-RAY DIFFRACTION98
5.1925-5.9260.19861450.17792686X-RAY DIFFRACTION98
5.926-7.39990.21661640.18992725X-RAY DIFFRACTION99
7.3999-19.71930.21721460.19052744X-RAY DIFFRACTION99
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)
10.00350.09370.04620.03830.05950.05870.12330.0993-0.24510.03990.0296-0.75150.00770.672300.40910.1010.15250.5586-0.08430.688444.1717.034119.3777
2-0.01480.0129-0.06240.02110.0273-0.00220.0649-0.29430.15620.27410.0344-0.39810.3166-0.016500.6158-0.1294-0.16040.68270.15380.72741.8335-6.529561.3214
30.0205-0.1522-0.064-0.0041-0.1160.04280.2907-0.2141-0.21640.84760.1214-0.63070.7420.17570-0.05940.07370.03210.1675-0.02820.148212.863743.999117.2015
4-0.0070.0404-0.07410.04450.0239-0.021-0.1421-0.3118-0.1638-0.1565-0.2179-0.06650.23240.503600.5440.20.25760.22880.02240.477614.0131.057624.4023
5-0.05560.0494-0.0699-0.01080.1243-0.02930.6239-0.80680.04190.5153-0.10490.0630.0948-1.0601-00.05140.20390.0750.1158-0.18650.2497-19.811452.294120.1823
6-0.05840.0026-0.1087-0.0592-0.04030.0224-0.0660.17910.1218-0.01020.17190.1508-0.1125-0.142-00.4677-0.08470.04760.3728-0.04280.3416-18.96418.466421.0622
70.05940.00130.0170.00820.02730.0394-0.0682-0.0134-0.0098-0.02650.09090.4525-0.38440.0163-00.6424-0.10130.09560.2805-0.07030.5189-48.767965.717256.2922
80.06280.0025-0.10920.1155-0.31170.1320.09880.71630.43480.5476-0.02330.6405-0.34-0.365300.1658-0.0713-0.19780.87080.14950.3531-50.550844.590317.7613
90.0179-0.0027-0.02070.0099-0.0078-0.0026-0.06420.0983-0.14950.0713-0.1363-0.06560.0059-0.1576-0-0.38240.0009-0.47820.336-0.10710.545844.39716.332145.6588
10-0.00180.00420.01670.01290.01530.00980.22610.0399-0.1696-0.36090.2972-0.4012-0.22240.0108-0-1.0321.0201-0.7785-0.15290.44110.107344.131916.200446.2366
110.0059-0.0058-0.02780.0052-0.0244-0.0016-0.1176-0.1379-0.1053-0.0188-0.15490.13590.24880.122500.17970.1966-0.25630.18020.7382-1.205413.927425.293437.7932
120.0120.02680.00530.0193-0.02310.02290.0165-0.1102-0.06990.28290.0391-0.0127-0.015-0.346200.290.21460.04740.26010.07570.246113.580724.725637.8372
130.0124-0.002-0.0352-0.0006-0.02150.00320.07230.066-0.0709-0.08660.0523-0.0220.17250.037100.14650.0098-0.03330.0932-0.09780.2114-18.773931.423137.7479
140.0024-0.0076-0.00230.0101-0.0237-0.0010.11630.11280.0720.0610.09680.1068-0.01150.153900.21650.00660.10370.0944-0.07350.3875-49.25640.211845.9477
150.0010.00880.00260.00060.03950.0006-0.15470.14150.12620.0916-0.1179-0.047-0.1950.148300.22660.03390.1101-0.1162-0.4395-0.161-49.427339.91745.3611
160.0159-0.00160.00820.0157-0.0318-0.0079-0.0299-0.020.0701-0.1124-0.15660.2487-0.0694-0.132200.2544-0.0059-0.03420.363-0.07840.0296-19.075930.856937.7666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L
13X-RAY DIFFRACTION13chain M
14X-RAY DIFFRACTION14chain O
15X-RAY DIFFRACTION15chain P
16X-RAY DIFFRACTION16chain N

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