[English] 日本語
Yorodumi
- PDB-3u5n: Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)... -

+
Open data


ID or keywords:

Loading...

-
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 H3.1Histone H3
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 / 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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'

+
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