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- PDB-3cbm: SET7/9-ER-AdoMet complex -

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Basic information

Entry
Database: PDB / ID: 3cbm
TitleSET7/9-ER-AdoMet complex
Components
  • Estrogen receptor
  • Histone-lysine N-methyltransferase SETD7
KeywordsTRANSFERASE/TRANSFERASE RECEPTOR / Estrogen receptor / protein lysine methylation / Activator / Chromatin regulator / Chromosomal protein / Methyltransferase / Nucleus / S-adenosyl-L-methionine / Transcription / Transcription regulation / Transferase / Alternative splicing / DNA-binding / Lipid-binding / Metal-binding / Phosphoprotein / Polymorphism / Steroid-binding / Zinc / Zinc-finger / TRANSFERASE-TRANSFERASE RECEPTOR COMPLEX
Function / homology
Function and homology information


peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / heterochromatin organization / PKMTs methylate histone lysines / p53 binding ...peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / heterochromatin organization / PKMTs methylate histone lysines / p53 binding / chromatin organization / chromosome / response to ethanol / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain ...Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Single Sheet / Beta Complex / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsCheng, X. / Jia, D.
CitationJournal: Mol.Cell / Year: 2008
Title: Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase.
Authors: Subramanian, K. / Jia, D. / Kapoor-Vazirani, P. / Powell, D.R. / Collins, R.E. / Sharma, D. / Peng, J. / Cheng, X. / Vertino, P.M.
History
DepositionFeb 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq
Item: _entity_name_com.name / _entity_src_gen.gene_src_common_name ..._entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num
Revision 1.3Aug 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Histone-lysine N-methyltransferase SETD7
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3446
Polymers29,7252
Non-polymers6194
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-6.4 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.338, 38.902, 66.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Histone-lysine N-methyltransferase SETD7 / Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET ...Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET domain-containing protein 7 / SET7/9


Mass: 28563.785 Da / Num. of mol.: 1 / Fragment: UNP residues 111-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Plasmid: pXC408 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)C+ / Keywords: catalytic domain
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Protein/peptide Estrogen receptor / ER / Estradiol receptor / ER-alpha / Nuclear receptor subfamily 3 group A member 1


Mass: 1161.419 Da / Num. of mol.: 1 / Fragment: UNP residues 298-307 / Source method: obtained synthetically / Details: ER peptide / Source: (synth.) synthetic construct (others) / Keywords: ER peptide
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growMethod: vapor diffusion / pH: 8
Details: 40-42.5% PEG3350, 100 mM Tris, pH 8.0, VAPOR DIFFUSION

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→25.59 Å / Num. obs: 27719 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.8
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2379 / % possible all: 83.7

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O9S

1o9s


Resolution: 1.69→25.59 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODELING. METHOD USED : FLAT MODEL KSOL : 0.366634 BSOL : 44.8929 (A**2)
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1355 -RANDOM
Rwork0.196 ---
obs-27719 90.4 %-
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2--0.76 Å20 Å2
3---0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-35 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.69→25.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 38 155 2204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 1.69→1.75 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.262 121 -
Rwork0.229 --
obs-2379 83.7 %

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