[English] 日本語
Yorodumi
- PDB-5a1l: Crystal structure of JmjC domain of human histone demethylase UTY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a1l
TitleCrystal structure of JmjC domain of human histone demethylase UTY with S21056a
ComponentsUBIQUITOUSLY TRANSCRIBED TETRATRICOPEPTIDE REPEAT PROTEIN Y-LINKED TRANSCRIPT VARIANT 57
KeywordsHYDROLASE
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / dioxygenase activity / histone demethylase activity / HDMs demethylate histones / chromatin DNA binding / heart development / regulation of gene expression / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / dioxygenase activity / histone demethylase activity / HDMs demethylate histones / chromatin DNA binding / heart development / regulation of gene expression / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Tetratricopeptide repeat ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Tetratricopeptide repeat / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribbon / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Chem-S2I / [histone H3]-trimethyl-L-lysine(27) demethylase / Histone demethylase UTY
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSrikannathasan, V. / Gileadi, C. / Johansson, C. / Krojer, T. / Tumber, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Brennan, P. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with S21056A
Authors: Srikannathasan, V. / Gileadi, C. / Johansson, C. / Krojer, T. / Tumber, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Brennan, P. / Oppermann, U.
History
DepositionMay 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUITOUSLY TRANSCRIBED TETRATRICOPEPTIDE REPEAT PROTEIN Y-LINKED TRANSCRIPT VARIANT 57
B: UBIQUITOUSLY TRANSCRIBED TETRATRICOPEPTIDE REPEAT PROTEIN Y-LINKED TRANSCRIPT VARIANT 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,68919
Polymers110,0132
Non-polymers1,67617
Water12,250680
1
A: UBIQUITOUSLY TRANSCRIBED TETRATRICOPEPTIDE REPEAT PROTEIN Y-LINKED TRANSCRIPT VARIANT 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,06213
Polymers55,0061
Non-polymers1,05512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UBIQUITOUSLY TRANSCRIBED TETRATRICOPEPTIDE REPEAT PROTEIN Y-LINKED TRANSCRIPT VARIANT 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6276
Polymers55,0061
Non-polymers6215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.711, 110.500, 119.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein UBIQUITOUSLY TRANSCRIBED TETRATRICOPEPTIDE REPEAT PROTEIN Y-LINKED TRANSCRIPT VARIANT 57 / HISTONE DEMETHYLASE UTY


Mass: 55006.402 Da / Num. of mol.: 2 / Fragment: JMJC DOMAIN, RESIDUES 799-1268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: F4MH27, UniProt: O14607*PLUS

-
Non-polymers , 5 types, 697 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-S2I / 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propan-1-ol


Mass: 375.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N5O
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.78 Å3/Da / Density % sol: 55.84 % / Description: NONE
Crystal growDetails: 25% PEG3350, 0.1M BIS-TRIS PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91742
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91742 Å / Relative weight: 1
ReflectionResolution: 2→29.31 Å / Num. obs: 81121 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZLI

3zli


Resolution: 2→81.12 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.548 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22493 4078 5 %RANDOM
Rwork0.18799 ---
obs0.18981 76980 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.275 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å20 Å2
2---0.55 Å20 Å2
3---3.01 Å2
Refinement stepCycle: LAST / Resolution: 2→81.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7044 0 104 680 7828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197334
X-RAY DIFFRACTIONr_bond_other_d0.0020.026852
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9459975
X-RAY DIFFRACTIONr_angle_other_deg0.898315716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80924.704338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.194151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6051530
X-RAY DIFFRACTIONr_chiral_restr0.0770.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021754
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_it1.7182.8563529
X-RAY DIFFRACTIONr_mcbond_other1.7182.8553528
X-RAY DIFFRACTIONr_mcangle_it2.7344.274406
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.223.1093805
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 290 -
Rwork0.292 5619 -
obs--98.73 %

+
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