[English] 日本語
Yorodumi
- PDB-5mr8: Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mr8
TitleCrystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K9ac histone peptide
Components
  • E3 ubiquitin-protein ligase TRIM33
  • Histone H3
KeywordsTRANSCRIPTION / Structural Genomics / Structural Genomics Consortium / SGC
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 / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / epigenetic regulation of gene expression / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / RING-type E3 ubiquitin transferase / 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 / Estrogen-dependent gene expression / 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 / Histone H3 signature 1. / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Bromodomain / 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 / Histone H3-7 / E3 ubiquitin-protein ligase TRIM33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsTallant, C. / Savitsky, P. / Fedorov, O. / Nunez-Alonso, G. / Siejka, P. / Krojer, T. / Williams, E. / Srikannathasan, V. / von Delft, F. / Arrowsmith, C.H. ...Tallant, C. / Savitsky, P. / Fedorov, O. / Nunez-Alonso, G. / Siejka, P. / Krojer, T. / Williams, E. / Srikannathasan, V. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K9ac histone peptide
Authors: Tallant, C. / Savitsky, P. / Fedorov, O. / Nunez-Alonso, G. / Siejka, P. / Krojer, T. / Williams, E. / Srikannathasan, V. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Category: diffrn_radiation_wavelength
Revision 1.2Jan 17, 2024Group: 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM33
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5104
Polymers23,3792
Non-polymers1312
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-3 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.885, 57.994, 71.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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: 22274.467 Da / Num. of mol.: 1 / Fragment: UNP residues 882-1073
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM33, KIAA1113, RFG7, TIF1G / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UPN9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Histone H3


Mass: 1104.283 Da / Num. of mol.: 1 / Fragment: UNP residues 2-10 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5TEC6, UniProt: P68431*PLUS
#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.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris pH 8.5, 25% PEG3350 / PH range: 8-8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.74→29.25 Å / Num. obs: 22066 / % possible obs: 98.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 33.055 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.024 / Net I/σ(I): 19.7
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 2.1 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U5M

3u5m


Resolution: 1.74→28.997 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.51
RfactorNum. reflection% reflection
Rfree0.2862 1071 4.89 %
Rwork0.2269 --
obs0.2299 21895 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.74→28.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 2 52 1626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051608
X-RAY DIFFRACTIONf_angle_d0.7922170
X-RAY DIFFRACTIONf_dihedral_angle_d3.227985
X-RAY DIFFRACTIONf_chiral_restr0.047234
X-RAY DIFFRACTIONf_plane_restr0.005280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7391-1.81820.321120.33262493X-RAY DIFFRACTION95
1.8182-1.91410.29661340.27032553X-RAY DIFFRACTION98
1.9141-2.0340.33211290.25372551X-RAY DIFFRACTION97
2.034-2.1910.32411310.24732572X-RAY DIFFRACTION98
2.191-2.41130.31091480.25392590X-RAY DIFFRACTION98
2.4113-2.760.31071320.26042618X-RAY DIFFRACTION98
2.76-3.47640.31941530.25392638X-RAY DIFFRACTION99
3.4764-29.0010.24541320.19032809X-RAY DIFFRACTION99
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)
15.0225-0.17051.78732.5065-1.5058.15720.16970.1493-0.2268-0.2-0.01390.07420.5628-0.175-0.05370.32450.0524-0.00250.1909-0.01190.290938.204143.503916.3664
25.50890.45725.77481.0997-0.1856.4176-0.34350.8843-0.1467-0.41640.45110.3949-0.3278-2.3846-0.26440.4621-0.12740.01151.19480.13330.515117.542244.514123.8506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 885 through 1070)
2X-RAY DIFFRACTION2(chain 'C' and resid 1 through 9)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more