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- PDB-4egc: Crystal Structure of MBP-fused Human Six1 Bound to Human Eya2 Eya... -

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Basic information

Entry
Database: PDB / ID: 4egc
TitleCrystal Structure of MBP-fused Human Six1 Bound to Human Eya2 Eya Domain
Components
  • Eyes absent homolog 2
  • Maltose-binding periplasmic protein, Homeobox protein SIX1 chimera
KeywordsTRANSCRIPTION/HYDROLASE / homeodomain (HD) / six domain (SD) / eya domain (ED) / haloacid dehalogenase (HAD) / transcription factor / co-activator / protein phosphatase / DNA binding / fusion protein / nucleus / TRANSCRIPTION-HYDROLASE complex
Function / homology
Function and homology information


regulation of skeletal muscle cell proliferation / fungiform papilla morphogenesis / mesonephric tubule formation / mesenchymal cell proliferation involved in ureter development / cellular response to 3,3',5-triiodo-L-thyronine / ureter smooth muscle cell differentiation / regulation of branch elongation involved in ureteric bud branching / positive regulation of secondary heart field cardioblast proliferation / olfactory placode formation / myotome development ...regulation of skeletal muscle cell proliferation / fungiform papilla morphogenesis / mesonephric tubule formation / mesenchymal cell proliferation involved in ureter development / cellular response to 3,3',5-triiodo-L-thyronine / ureter smooth muscle cell differentiation / regulation of branch elongation involved in ureteric bud branching / positive regulation of secondary heart field cardioblast proliferation / olfactory placode formation / myotome development / regulation of skeletal muscle cell differentiation / mesodermal cell fate specification / striated muscle tissue development / positive regulation of ureteric bud formation / facial nerve morphogenesis / otic vesicle development / regulation of synaptic assembly at neuromuscular junction / positive regulation of mesenchymal cell proliferation involved in ureter development / mitochondrial outer membrane permeabilization / trigeminal ganglion development / myoblast migration / cochlea morphogenesis / aorta morphogenesis / metanephric mesenchyme development / neuron fate specification / regulation of skeletal muscle satellite cell proliferation / Formation of the ureteric bud / endothelin receptor signaling pathway / embryonic skeletal system morphogenesis / positive regulation of myoblast proliferation / positive regulation of branching involved in ureteric bud morphogenesis / pharyngeal system development / pattern specification process / organ induction / regulation of epithelial cell proliferation / embryonic cranial skeleton morphogenesis / myoblast proliferation / neural crest cell differentiation / regulation of neuron differentiation / middle ear morphogenesis / ureteric bud development / inner ear morphogenesis / branching involved in ureteric bud morphogenesis / generation of neurons / detection of maltose stimulus / maltose transport complex / inner ear development / outflow tract morphogenesis / carbohydrate transport / thyroid gland development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / carbohydrate transmembrane transporter activity / maltose binding / protein localization to nucleus / maltose transport / maltodextrin transmembrane transport / skeletal muscle tissue development / skeletal muscle fiber development / extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Notch signaling pathway / positive regulation of brown fat cell differentiation / epithelial cell differentiation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / ATP-binding cassette (ABC) transporter complex / positive regulation of DNA repair / thymus development / kidney development / cell chemotaxis / sensory perception of sound / transcription coactivator binding / sequence-specific double-stranded DNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / outer membrane-bounded periplasmic space / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / transcription regulator complex / negative regulation of neuron apoptotic process / sequence-specific DNA binding / cell differentiation / periplasmic space / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / apoptotic process / DNA damage response / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Homeobox protein SIX1, N-terminal SD domain / Transcriptional regulator, SIX1, N-terminal SD domain / Rossmann fold - #12350 / EYA domain / Eyes absent family / EYA domain superfamily / EYA domain, metazoan / Homeobox KN domain / Homeobox KN domain / Homeobox, conserved site ...Homeobox protein SIX1, N-terminal SD domain / Transcriptional regulator, SIX1, N-terminal SD domain / Rossmann fold - #12350 / EYA domain / Eyes absent family / EYA domain superfamily / EYA domain, metazoan / Homeobox KN domain / Homeobox KN domain / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / haloacid dehalogenase-like hydrolase / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / HAD-like superfamily / Periplasmic binding protein-like II / Homeobox-like domain superfamily / D-Maltodextrin-Binding Protein; domain 2 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Protein phosphatase EYA2 / Maltose/maltodextrin-binding periplasmic protein / Homeobox protein SIX1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.994 Å
AuthorsZhao, R. / Patrick, A.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure-function analyses of the human SIX1-EYA2 complex reveal insights into metastasis and BOR syndrome.
Authors: Patrick, A.N. / Cabrera, J.H. / Smith, A.L. / Chen, X.S. / Ford, H.L. / Zhao, R.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, Homeobox protein SIX1 chimera
B: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8964
Polymers95,5292
Non-polymers3672
Water14,628812
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-10 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.207, 150.180, 53.921
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1140-

HOH

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Components

#1: Protein Maltose-binding periplasmic protein, Homeobox protein SIX1 chimera / MBP / MMBP / Maltodextrin-binding protein / Sine oculis homeobox homolog 1


Mass: 62502.996 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: E172A,N173A,E359A,K362A,D363A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: b4034, JW3994, malE, MBP, SIX1 / Plasmid: PMALX_B / Production host: Escherichia coli (E. coli) / Strain (production host): XA-90 / References: UniProt: P0AEX9, UniProt: Q15475
#2: Protein Eyes absent homolog 2 / EYA2


Mass: 33026.348 Da / Num. of mol.: 1 / Fragment: Eya domain (UNP residues 253-538)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EAB1, EYA2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA-90 / References: UniProt: O00167, protein-tyrosine-phosphatase
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A IS A CHIMERA (MBP FUSION) COMPRISING RESIDUES 27-392 OF UNP P0AEX9 AND RESIDUES 1-189 OF UNP Q15475.

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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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 13.75% PEG8000, 0.01 M magnesium chloride, 0.05 M MES, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 145786 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.081 / Χ2: 0.841 / Net I/σ(I): 4.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.48-1.511.432710.828139.8
1.51-1.531.539150.698147.4
1.53-1.561.645670.545155.6
1.56-1.591.753411.286164.9
1.59-1.632.364780.954178.5
1.63-1.673.673770.697189.6
1.67-1.715.777960.651194.8
1.71-1.757.779010.672195.7
1.75-1.818.479520.682196.1
1.81-1.868.680320.697196.7
1.86-1.938.680100.73197.3
1.93-2.018.680820.762197.60.702
2.01-2.18.681430.779197.90.456
2.1-2.218.682100.797198.90.327
2.21-2.358.582780.804199.40.233
2.35-2.538.683270.823199.80.169
2.53-2.798.783610.987199.90.129
2.79-3.198.784531.20311000.089
3.19-4.028.884731.09111000.047
4.02-50988190.944199.70.031

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.994→36.032 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 3488 5.08 %
Rwork0.184 --
obs0.1861 68728 99.51 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.077 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 104.35 Å2 / Biso mean: 30.673 Å2 / Biso min: 13.02 Å2
Baniso -1Baniso -2Baniso -3
1--6.8795 Å20 Å20 Å2
2--3.4778 Å20 Å2
3---3.4016 Å2
Refinement stepCycle: LAST / Resolution: 1.994→36.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6295 0 24 812 7131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076467
X-RAY DIFFRACTIONf_angle_d1.0458761
X-RAY DIFFRACTIONf_chiral_restr0.069955
X-RAY DIFFRACTIONf_plane_restr0.0041125
X-RAY DIFFRACTIONf_dihedral_angle_d12.5462377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.994-2.02170.29061220.22972385250793
2.0217-2.05060.2621320.21625712703100
2.0506-2.08120.2761350.211525882723100
2.0812-2.11370.28111290.210725662695100
2.1137-2.14840.24971290.211326302759100
2.1484-2.18540.26041370.205125812718100
2.1854-2.22510.29581360.207325742710100
2.2251-2.26790.26311500.205725942744100
2.2679-2.31420.26011300.207826132743100
2.3142-2.36450.32251340.200425862720100
2.3645-2.41950.25011210.197426092730100
2.4195-2.480.2561450.201825802725100
2.48-2.54710.27171530.204325902743100
2.5471-2.6220.25161200.206726132733100
2.622-2.70660.24271730.182125922765100
2.7066-2.80330.23781360.195226032739100
2.8033-2.91550.22881420.194525852727100
2.9155-3.04810.25951350.19526322767100
3.0481-3.20870.21941260.18926492775100
3.2087-3.40960.231450.184526392784100
3.4096-3.67260.21211480.168726162764100
3.6726-4.04180.18671450.159826432788100
4.0418-4.62560.17251730.144226602833100
4.6256-5.82380.18151350.16327162851100
5.8238-36.03780.19061570.18582825298299

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