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- PDB-4mhv: Crystal structure of the PNT domain of human ETS2 -

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Basic information

Entry
Database: PDB / ID: 4mhv
TitleCrystal structure of the PNT domain of human ETS2
ComponentsProtein C-ets-2
KeywordsTRANSCRIPTION / PNT (pointed) domain / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


ectodermal cell fate commitment / primitive streak formation / nuclear glucocorticoid receptor binding / mesoderm development / skeletal system development / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...ectodermal cell fate commitment / primitive streak formation / nuclear glucocorticoid receptor binding / mesoderm development / skeletal system development / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Transforming protein C-ets-2 / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 1. ...Transforming protein C-ets-2 / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Protein C-ets-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.45 Å
AuthorsNewman, J.A. / Cooper, C.D.O. / Krojer, T. / Shrestha, L. / Burgess-brown, N. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Gileadi, O.
CitationJournal: To be Published
Title: Crystal structure of the PNT domain of human ETS2
Authors: Newman, J.A. / Cooper, C.D.O. / Krojer, T. / Shrestha, L. / Burgess-brown, N. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Gileadi, O.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Other
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_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_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: Protein C-ets-2
B: Protein C-ets-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2058
Polymers22,7702
Non-polymers4346
Water543
1
A: Protein C-ets-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5764
Polymers11,3851
Non-polymers1913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein C-ets-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6284
Polymers11,3851
Non-polymers2433
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.440, 64.440, 263.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Protein C-ets-2


Mass: 11385.207 Da / Num. of mol.: 2 / Fragment: PNT domain (UNP residues 76-170)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P15036
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 3.47 Å3/Da / Density % sol: 64.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Cacadylate, pH 6.5, 14 % PEG 10K, 20 % Glycerol, 0.16 M Calcium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→47 Å / Num. all: 12894 / Num. obs: 12894 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 57.02 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.8
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.015 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.11.4refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.45→43.95 Å / Cor.coef. Fo:Fc: 0.8953 / Cor.coef. Fo:Fc free: 0.9235 / SU R Cruickshank DPI: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 615 4.89 %RANDOM
Rwork0.2304 ---
obs0.2307 12589 98.21 %-
all-12589 --
Displacement parametersBiso mean: 93.55 Å2
Baniso -1Baniso -2Baniso -3
1--18.7832 Å20 Å20 Å2
2---18.7832 Å20 Å2
3---37.5664 Å2
Refine analyzeLuzzati coordinate error obs: 0.609 Å
Refinement stepCycle: LAST / Resolution: 2.45→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 27 3 1550
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011585HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.22141HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d546SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes223HARMONIC5
X-RAY DIFFRACTIONt_it1585HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion20.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1189SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11828SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.68 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2569 136 4.95 %
Rwork0.2467 2613 -
all0.2471 2749 -
obs--98.21 %
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)
17.9631-1.10894.27512.7859-0.72310.14750.56940.3124-0.4596-0.472-0.105-0.07330.25661.3031-0.46440.02850.4065-0.08550.057-0.1357-0.325832.188930.906631.4518
23.5256-1.75631.70143.3673-0.668310.28030.28270.6468-0.3676-0.34540.0160.18880.64571.0585-0.29870.06140.2235-0.122-0.169-0.0376-0.302317.197935.883512.3247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A77 - 170
2X-RAY DIFFRACTION2B75 - 170

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