[English] 日本語
Yorodumi
- PDB-4iej: Crystal structure of a DNA methyltransferase 1 associated protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iej
TitleCrystal structure of a DNA methyltransferase 1 associated protein 1 (DMAP1) from Homo sapiens at 1.45 A resolution
ComponentsDNA methyltransferase 1-associated protein 1
KeywordsTRANSCRIPTION / DNA methylation / chromatin regulator / repressor / Structural Genomics / Joint Center for Structural Genomics / JCSG / Partnership for T-Cell Biology / TCELL / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Swr1 complex / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / replication fork / positive regulation of protein import into nucleus / transcription corepressor activity / nucleosome / HATs acetylate histones / response to ethanol ...Swr1 complex / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / replication fork / positive regulation of protein import into nucleus / transcription corepressor activity / nucleosome / HATs acetylate histones / response to ethanol / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / regulation of cell cycle / chromatin remodeling / DNA repair / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA methyltransferase 1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a DNA methyltransferase 1 associated protein 1 (DMAP1) from Homo sapiens at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Structure summary
Revision 1.2Jan 16, 2013Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA methyltransferase 1-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2572
Polymers11,2171
Non-polymers401
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.353, 37.353, 229.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

-
Components

#1: Protein DNA methyltransferase 1-associated protein 1 / DNMAP1 / DNMT1-associated protein 1


Mass: 11216.549 Da / Num. of mol.: 1 / Fragment: SANT domain containing residues 121-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC008053, DMAP1, KIAA1425 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9NPF5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (121-212) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (121-212) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.20M calcium chloride 20.00% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors, liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→38.327 Å / Num. obs: 18199 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.311 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.99
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.45-1.50.9842.3157701696199.7
1.5-1.560.7573159011763199.9
1.56-1.630.5334.2155651733199.9
1.63-1.720.356.4171241837199.8
1.72-1.830.2399.3163321804199.9
1.83-1.970.1414.3157161775199.4
1.97-2.170.0823.51679518181100
2.17-2.480.05332.4156031799199.4
2.48-3.120.04341.4165701880199.9
3.12-38.3270.03546159132094199.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
MOLREPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hm5

3hm5


Resolution: 1.45→38.327 Å / Cor.coef. Fo:Fc: 0.9512 / Cor.coef. Fo:Fc free: 0.9482 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. CALCIUM ION MODELED IS PRESENT IN CRYSTALLIZATION BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 920 5.09 %RANDOM
Rwork0.197 ---
obs0.1984 18079 99.78 %-
Displacement parametersBiso max: 112.38 Å2 / Biso mean: 36.2049 Å2 / Biso min: 17.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.9136 Å20 Å20 Å2
2---2.9136 Å20 Å2
3---5.8272 Å2
Refine analyzeLuzzati coordinate error obs: 0.251 Å
Refinement stepCycle: LAST / Resolution: 1.45→38.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms655 0 1 76 732
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d371SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes23HARMONIC2
X-RAY DIFFRACTIONt_gen_planes120HARMONIC5
X-RAY DIFFRACTIONt_it747HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion89SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact882SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d747HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1023HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion2.9
LS refinement shellResolution: 1.45→1.54 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.234 163 5.8 %
Rwork0.2231 2649 -
all0.2237 2812 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: 4.3298 Å / Origin y: 24.2719 Å / Origin z: 6.973 Å
111213212223313233
T-0.0424 Å20.0191 Å2-0.0041 Å2--0.0414 Å2-0.0109 Å2---0.108 Å2
L1.1018 °2-0.0185 °20.3331 °2-2.143 °2-0.045 °2--6.3766 °2
S-0.0223 Å °-0.036 Å °-0.0515 Å °0.1197 Å °-0.0648 Å °-0.0139 Å °-0.1 Å °-0.4342 Å °0.0871 Å °
Refinement TLS groupSelection details: { A|133 - A|207 }

+
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