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- PDB-2qic: Crystal Structure of the ING1 PHD Finger in complex with a Histon... -

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Basic information

Entry
Database: PDB / ID: 2qic
TitleCrystal Structure of the ING1 PHD Finger in complex with a Histone H3K4ME3 peptide
Components
  • H3K4ME3 PEPTIDE
  • Inhibitor of growth protein 1
KeywordsANTITUMOR PROTEIN / APOPTOSIS / PHD / ING1 / HISTONE / H3K4ME3 / CHROMATIN
Function / homology
Function and homology information


regulation of response to osmotic stress / phosphorelay signal transduction system / plasma membrane => GO:0005886 / phosphorelay sensor kinase activity
Similarity search - Function
Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Histidine kinase domain / Histidine kinase domain profile. / Herpes Virus-1 ...Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Histidine kinase domain / Histidine kinase domain profile. / Herpes Virus-1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sensor histidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body Refinement / Resolution: 2.1 Å
AuthorsPena, P.V. / Champagne, K. / Zhao, R. / Kutateladze, T.G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor.
Authors: Pena, P.V. / Hom, R.A. / Hung, T. / Lin, H. / Kuo, A.J. / Wong, R.P. / Subach, O.M. / Champagne, K.S. / Zhao, R. / Verkhusha, V.V. / Li, G. / Gozani, O. / Kutateladze, T.G.
History
DepositionJul 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn_type / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_conn_type.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: Inhibitor of growth protein 1
B: H3K4ME3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5574
Polymers8,4262
Non-polymers1312
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Inhibitor of growth protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2073
Polymers7,0761
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: H3K4ME3 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)1,3511
Polymers1,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.060, 49.060, 52.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Inhibitor of growth protein 1


Mass: 7075.926 Da / Num. of mol.: 1 / Fragment: PHD DOMAIN (RESIDUES 345-404)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ING1 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9UK53
#2: Protein/peptide H3K4ME3 PEPTIDE


Mass: 1350.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic PEPTIDE H3K4ME3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.01 M NiCl2 6H20, 0.1 M Tris, 20% polyethylene glycol monomethyl ether 2K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.257 Å
DetectorDetector: AREA DETECTOR / Date: Feb 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.257 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 4526 / Num. obs: 4526 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 9.35 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9.78 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.4 / Num. unique all: 450 / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: Rigid Body Refinement
Starting model: PDB entry 2G6Q

2g6q


Resolution: 2.1→25 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.264 473 -RANDOM
Rwork0.24 ---
all-4526 --
obs-4526 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms477 0 2 41 520
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.091
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection% reflection
Rfree0.33 62 -
Rwork0.281 --
obs-448 100 %

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