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- PDB-3u5p: Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)... -

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Basic information

Entry
Database: PDB / ID: 3u5p
TitleCrystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide
Components
  • E3 ubiquitin-protein ligase TRIM33
  • Histone H3.1Histone H3
KeywordsTRANSCRIPTION / TRIM33 / PHD / Bromodomain / TGF-beta / epigenetics / histone / methylation / K9me3 / K14ac / K18ac / K23ac
Function / homology
Function and homology information


co-SMAD binding / regulation of transforming growth factor beta receptor signaling pathway / Germ layer formation at gastrulation / R-SMAD binding / negative regulation of BMP signaling pathway / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling ...co-SMAD binding / regulation of transforming growth factor beta receptor signaling pathway / Germ layer formation at gastrulation / R-SMAD binding / negative regulation of BMP signaling pathway / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RING-type E3 ubiquitin transferase / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin-protein transferase activity / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein ubiquitination / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Bromodomain-like / Zinc finger RING-type profile. / Histone Acetyltransferase; Chain A / Zinc finger, RING-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / E3 ubiquitin-protein ligase TRIM33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, Z. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: A poised chromatin platform for TGF-beta access to master regulators
Authors: Xi, Q. / Wang, Z. / Zaromytidou, A.I. / Zhang, X.H. / Chow-Tsang, L.F. / Liu, J.X. / Kim, H. / Barlas, A. / Manova-Todorova, K. / Kaartinen, V. / Studer, L. / Mark, W. / Patel, D.J. / Massague, J.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Source and taxonomy
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_auth_seq_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM33
I: Histone H3.1
B: E3 ubiquitin-protein ligase TRIM33
J: Histone H3.1
C: E3 ubiquitin-protein ligase TRIM33
K: Histone H3.1
D: E3 ubiquitin-protein ligase TRIM33
L: Histone H3.1
E: E3 ubiquitin-protein ligase TRIM33
M: Histone H3.1
F: E3 ubiquitin-protein ligase TRIM33
N: Histone H3.1
G: E3 ubiquitin-protein ligase TRIM33
O: Histone H3.1
H: E3 ubiquitin-protein ligase TRIM33
P: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,07032
Polymers216,02416
Non-polymers1,04716
Water0
1
A: E3 ubiquitin-protein ligase TRIM33
I: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1344
Polymers27,0032
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-9 kcal/mol
Surface area11470 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase TRIM33
J: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1344
Polymers27,0032
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-9 kcal/mol
Surface area11470 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase TRIM33
K: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1344
Polymers27,0032
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-8 kcal/mol
Surface area11400 Å2
MethodPISA
4
D: E3 ubiquitin-protein ligase TRIM33
L: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1344
Polymers27,0032
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-9 kcal/mol
Surface area11330 Å2
MethodPISA
5
E: E3 ubiquitin-protein ligase TRIM33
M: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1344
Polymers27,0032
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-10 kcal/mol
Surface area11570 Å2
MethodPISA
6
F: E3 ubiquitin-protein ligase TRIM33
N: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1344
Polymers27,0032
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-9 kcal/mol
Surface area11390 Å2
MethodPISA
7
G: E3 ubiquitin-protein ligase TRIM33
O: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1344
Polymers27,0032
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-8 kcal/mol
Surface area11390 Å2
MethodPISA
8
H: E3 ubiquitin-protein ligase TRIM33
P: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1344
Polymers27,0032
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-8 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.426, 63.608, 124.611
Angle α, β, γ (deg.)90.01, 90.04, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
E3 ubiquitin-protein ligase TRIM33 / Ectodermin homolog / RET-fused gene 7 protein / Protein Rfg7 / Transcription intermediary factor 1- ...Ectodermin homolog / RET-fused gene 7 protein / Protein Rfg7 / Transcription intermediary factor 1-gamma / TIF1-gamma / Tripartite motif-containing protein 33


Mass: 23830.262 Da / Num. of mol.: 8 / Fragment: The PHD and Bromo domain of TRIM33
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM33, KIAA1113, RFG7, TIF1G / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UPN9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide
Histone H3.1 / Histone H3 / Histone H3


Mass: 3172.708 Da / Num. of mol.: 8
Fragment: N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 197 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2011
RadiationMonochromator: SI mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 47438 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 52.6 Å2 / Rsym value: 0.047 / Net I/σ(I): 26.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4785 / Rsym value: 0.41 / % possible all: 98

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U5M

3u5m


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 39.494 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26478 2264 5 %RANDOM
Rwork0.21048 ---
obs0.21317 43152 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.357 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.14 Å20.18 Å2
2---0.5 Å2-0.05 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13245 0 16 0 13261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213529
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.97618248
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83751605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37724.368625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.085152386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2781572
X-RAY DIFFRACTIONr_chiral_restr0.0980.21981
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.865 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 154 -
Rwork0.344 2774 -
obs--81.65 %
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)
15.35470.40343.87192.37530.45756.8915-0.6024-0.74310.86350.11510.04160.3396-0.5941-1.26980.56080.17110.177-0.00320.4614-0.15670.299414.917-3.1110.666
25.5928-0.66694.03692.454-0.70366.5992-0.61860.73930.9331-0.08730.0203-0.3936-0.53421.25590.59830.1592-0.1613-0.01950.48350.1780.3249-15.546-34.9185.144
35.12910.3574-3.64632.3594-0.45476.5194-0.6099-0.7195-0.83160.06770.039-0.32680.58221.1910.57090.17490.1646-0.0060.47790.15630.303616.188-18.32-51.626
45.3429-0.3601-3.84752.00690.35636.5287-0.56990.6843-0.8179-0.09610.08120.30560.5881-1.13950.48870.1598-0.1505-0.01420.4455-0.13740.2866-16.75-50.104-57.173
52.613-0.5585-0.65975.23673.86316.64610.0346-0.0868-0.40030.7096-0.6570.92551.2668-0.58110.62240.4753-0.16460.15630.220.01050.348.028-11.329-82.804
61.66010.2520.13994.72393.60546.64440.08810.13390.2834-0.6663-0.55730.7611-1.1972-0.59940.46920.44420.1863-0.1780.21570.01410.3206-23.698-41.883-88.315
71.9858-0.36580.39565.2123-3.53076.61330.1005-0.10870.33450.6708-0.5669-0.8072-1.17880.60560.46640.4354-0.178-0.15950.1756-0.0060.3177-40.267-10.086-20.481
81.95340.4085-0.37455.4157-3.75936.47890.09740.0988-0.3602-0.6818-0.6439-0.79771.17970.63120.54650.41730.18210.14390.2077-0.01610.3123-8.545-43.119-26.003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A884 - 1087
2X-RAY DIFFRACTION2B884 - 1087
3X-RAY DIFFRACTION3C884 - 1087
4X-RAY DIFFRACTION4D884 - 1087
5X-RAY DIFFRACTION5E884 - 1087
6X-RAY DIFFRACTION6F884 - 1087
7X-RAY DIFFRACTION7G884 - 1087
8X-RAY DIFFRACTION8H884 - 1087

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