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- PDB-3u5o: Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)... -

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Basic information

Entry
Database: PDB / ID: 3u5o
TitleCrystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide
Components
  • E3 ubiquitin-protein ligase TRIM33
  • Histone H3.1Histone H3
KeywordsTRANSCRIPTION / TRIM33 / PHD / Bromodomain / TGF-beta / epigenetics / histone / methylation / K9me3 / K14ac / K18ac
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: 2.7 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 1.1Sep 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 1.2Dec 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
B: E3 ubiquitin-protein ligase TRIM33
C: E3 ubiquitin-protein ligase TRIM33
D: E3 ubiquitin-protein ligase TRIM33
E: E3 ubiquitin-protein ligase TRIM33
F: E3 ubiquitin-protein ligase TRIM33
G: E3 ubiquitin-protein ligase TRIM33
H: E3 ubiquitin-protein ligase TRIM33
I: Histone H3.1
J: Histone H3.1
K: Histone H3.1
L: Histone H3.1
M: Histone H3.1
N: Histone H3.1
O: Histone H3.1
P: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,58432
Polymers210,53716
Non-polymers1,04716
Water0
1
A: E3 ubiquitin-protein ligase TRIM33
I: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,3172
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-8 kcal/mol
Surface area11900 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase TRIM33
J: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,3172
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-10 kcal/mol
Surface area11770 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase TRIM33
K: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,3172
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-10 kcal/mol
Surface area12430 Å2
MethodPISA
4
D: E3 ubiquitin-protein ligase TRIM33
L: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,3172
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-8 kcal/mol
Surface area11510 Å2
MethodPISA
5
E: E3 ubiquitin-protein ligase TRIM33
M: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,3172
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-9 kcal/mol
Surface area11760 Å2
MethodPISA
6
F: E3 ubiquitin-protein ligase TRIM33
N: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,3172
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-10 kcal/mol
Surface area11840 Å2
MethodPISA
7
G: E3 ubiquitin-protein ligase TRIM33
O: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,3172
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-8 kcal/mol
Surface area11590 Å2
MethodPISA
8
H: E3 ubiquitin-protein ligase TRIM33
P: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,3172
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-9 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.639, 63.650, 125.195
Angle α, β, γ (deg.)90.05, 89.98, 89.93
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: 2486.892 Da / Num. of mol.: 8
Fragment: N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 197 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2011
RadiationMonochromator: SI mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 52739 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 54.1 Å2 / Rsym value: 0.052 / Net I/σ(I): 39.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 5307 / Rsym value: 0.582 / % possible all: 98.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O33

3o33


Resolution: 2.7→28.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.91 / SU B: 35.428 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27972 1932 3.8 %RANDOM
Rwork0.20456 ---
obs0.20748 48277 93.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.953 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0.38 Å2-0.05 Å2
2---1.01 Å2-0.39 Å2
3---2.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13506 0 16 0 13522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213795
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.97518616
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65251644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.02824.517642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.44152436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8771572
X-RAY DIFFRACTIONr_chiral_restr0.1040.22022
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110336
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: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 102 -
Rwork0.249 2867 -
obs--74.94 %
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)
11.46660.37740.55152.96152.63915.58030.1770.31680.3307-0.417-0.50250.4703-1.009-0.36190.32550.57180.168-0.07790.26170.0910.32312.431-14.985-10.82
21.35980.1441-0.13062.26211.87624.43330.2265-0.43290.00840.206-0.09290.00270.28010.5013-0.13350.3614-0.04640.08450.29260.06230.1481-19.022-37.6620.314
33.25110.0926-2.42431.36160.15755.8488-0.50120.4879-0.5249-0.28030.1780.24130.3314-1.06320.32320.2098-0.0925-0.07710.4927-0.09020.28669.147-23.50920.42
42.720.3804-2.38471.5225-0.30335.0429-0.4974-0.3784-0.44550.33190.1833-0.34670.31110.9110.3140.2750.1564-0.08550.52530.10340.3475-20.3248.10126.142
53.45790.41433.08361.22790.49595.6995-0.5208-0.50820.51590.3090.15650.2602-0.3452-1.06060.36430.25870.17140.06790.5158-0.07960.3044-22.394-39.936-36.861
63.0667-0.2232.69561.554-0.34135.6573-0.48230.47690.5221-0.30070.1658-0.342-0.36130.98210.31650.2223-0.09190.07520.48340.10490.290810.91-8.137-42.05
71.56750.3275-0.27672.9897-2.19515.55960.1410.2383-0.3173-0.4062-0.4206-0.51331.05880.37020.27970.52730.1810.0930.1976-0.05990.308317.761-16.72251.742
81.6376-0.17550.51643.7252-3.0496.04130.1953-0.34070.33950.4565-0.5829-0.4546-0.97160.33080.38760.517-0.1041-0.07990.2072-0.0730.3011-14.073-47.10456.933
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A883 - 1087
2X-RAY DIFFRACTION2H883 - 1087
3X-RAY DIFFRACTION3B883 - 1087
4X-RAY DIFFRACTION4C883 - 1087
5X-RAY DIFFRACTION5D883 - 1087
6X-RAY DIFFRACTION6E883 - 1087
7X-RAY DIFFRACTION7F883 - 1087
8X-RAY DIFFRACTION8G883 - 1087

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