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- PDB-3u5n: Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)... -

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Basic information

Entry
Database: PDB / ID: 3u5n
TitleCrystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)K9me3K14ac histone peptide
Components
  • E3 ubiquitin-protein ligase TRIM33
  • Histone H3.1
KeywordsTRANSCRIPTION / TRIM33 / PHD / Bromodomain / TGF-beta / epigenetics / histone / methylation / K9me3 / K14ac
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 / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...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 / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / RING-type E3 ubiquitin transferase / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / ubiquitin-protein transferase activity / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / protein ubiquitination / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
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, PHD-type, conserved site / PHD-finger ...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, PHD-type, conserved site / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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: 1.95 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
C: Histone H3.1
B: E3 ubiquitin-protein ligase TRIM33
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4708
Polymers52,2084
Non-polymers2624
Water3,819212
1
A: E3 ubiquitin-protein ligase TRIM33
C: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2354
Polymers26,1042
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-3 kcal/mol
Surface area11170 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase TRIM33
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2354
Polymers26,1042
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-2 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.586, 113.737, 39.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2
Fragment: The C-terminal PHD and Bromo dual domains of TRIM33, UNP residues 882-1087
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM33, KIAA1113, RFG7, TIF1G / Plasmid details: ?469008 / 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


Mass: 2273.682 Da / Num. of mol.: 2
Fragment: N-terminal histone H3 peptide containing trimethylated K9 and acetylated K14, UNP residues 2-21
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.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M ammonium tartrate 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: 1.28215 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2011
RadiationMonochromator: SI mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28215 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 32561 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.091 / Net I/σ(I): 24.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 32561 / Rsym value: 0.495 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U5M

3u5m


Resolution: 1.95→29.792 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1651 5.08 %Random
Rwork0.2024 ---
obs0.2051 32513 97.4 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.925 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.8189 Å20 Å2-0 Å2
2--19.4168 Å20 Å2
3----8.5979 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 4 212 3443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083295
X-RAY DIFFRACTIONf_angle_d1.0834446
X-RAY DIFFRACTIONf_dihedral_angle_d18.5211250
X-RAY DIFFRACTIONf_chiral_restr0.082484
X-RAY DIFFRACTIONf_plane_restr0.005570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00390.35641320.29022362X-RAY DIFFRACTION91
2.0039-2.06860.34661260.24612591X-RAY DIFFRACTION99
2.0686-2.14250.29071400.21212579X-RAY DIFFRACTION100
2.1425-2.22830.2221360.20262597X-RAY DIFFRACTION99
2.2283-2.32960.23071580.19342565X-RAY DIFFRACTION99
2.3296-2.45240.25691480.2042585X-RAY DIFFRACTION99
2.4524-2.6060.26371310.20432582X-RAY DIFFRACTION99
2.606-2.80710.31191070.20762632X-RAY DIFFRACTION99
2.8071-3.08930.27871630.22392574X-RAY DIFFRACTION98
3.0893-3.53570.25321300.19562591X-RAY DIFFRACTION97
3.5357-4.45220.20911480.18042576X-RAY DIFFRACTION96
4.4522-29.79520.25731320.19542628X-RAY DIFFRACTION93
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)
10.0711-0.0549-0.01910.08870.02190.03490.0043-0.13270.1125-0.0057-0.0222-0.17080.06080.3252-00.13750.0487-0.00260.21430.00490.1831.6079-10.59454.1595
20.03180.01420.01440.06370.01640.02830.06960.3411-0.0384-0.1478-0.203-0.22040.13260.239300.15490.06150.03410.19670.01580.1667-9.8088-3.8908-2.4676
30.2172-0.0157-0.07980.39980.08790.18560.0360.0712-0.03480.0013-0.0455-0.0008-0.0186-0.117200.14540.00560.00140.1277-0.01320.1077-22.2058-14.41438.2142
40.0195-0.01090.00760.010.01270.0131-0.017-0.0247-0.10440.05220.02570.0882-0.03880.02400.24190.0725-0.00120.60520.04290.34866.9984-18.05188.1439
50.02060.00940.00570.02690.01240.0234-0.0575-0.07170.0233-0.0149-0.01770.1198-0.2105-0.2227-00.2088-0.0023-0.04370.30850.11180.3347-27.4786-37.2241-3.6895
60.0235-0.029-0.06380.00160.00830.04910.5395-0.3583-0.3699-0.0793-0.04880.22210.2987-0.3255-00.0922-0.35810.0992-0.46160.8691-0.2519-18.9934-47.69262.5018
70.0210.03960.01660.019-0.02180.04320.0890.48440.0016-0.02570.0752-0.0411-0.12930.037600.2383-0.01920.0140.29240.02350.237-3.3601-38.7879-12.3099
8-0.0052-0.00370.0032-0.00240.00680.0007-0.00470.0768-0.0522-0.1740.06370.03440.1816-0.056900.3918-0.001-0.11440.14040.05070.6668-6.1845-54.5271-3.3318
90.04990.01250.03180.0050.00810.02410.0702-0.11960.01270.15-0.0358-0.1358-0.18080.068700.19770.0022-0.0030.19350.00630.2184.5119-34.548-7.4648
100.0802-0.0251-0.00070.0250.03060.03330.094-0.20640.04380.091-0.1664-0.1373-0.1271-0.0755-00.2698-0.0080.020.32450.03720.2417-3.6038-33.97452.6791
110.02550.01170.0382-0.0238-0.074-0.02090.0093-0.164-0.2488-0.25770.02110.084-0.3677-0.0973-00.262-0.0671-0.00910.34890.00950.2763-27.6394-30.7281-12.0473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 883:932)
2X-RAY DIFFRACTION2chain 'A' and (resseq 933:975)
3X-RAY DIFFRACTION3chain 'A' and (resseq 976:1087)
4X-RAY DIFFRACTION4chain 'J'
5X-RAY DIFFRACTION5chain 'B' and (resseq 883:912)
6X-RAY DIFFRACTION6chain 'B' and (resseq 913:975)
7X-RAY DIFFRACTION7chain 'B' and (resseq 976:1009)
8X-RAY DIFFRACTION8chain 'B' and (resseq 1010:1020)
9X-RAY DIFFRACTION9chain 'B' and (resseq 1021:1048)
10X-RAY DIFFRACTION10chain 'B' and (resseq 1049:1087)
11X-RAY DIFFRACTION11chain 'E'

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