[English] 日本語
Yorodumi
- PDB-4x9j: EGR-1 with Doubly Methylated DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x9j
TitleEGR-1 with Doubly Methylated DNA
Components
  • DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3')
  • DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*(5CM)P*GP*C)-3')
  • Early growth response protein 1
KeywordsTranscription Regulator/DNA / DNA Binding / Methylated DNA / ZINC FINGER / TRANSCRIPTION / Transcription Regulator-DNA complex
Function / homology
Function and homology information


regulation of protein sumoylation / glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...regulation of protein sumoylation / glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / positive regulation of gene expression via chromosomal CpG island demethylation / NGF-stimulated transcription / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / skeletal muscle cell differentiation / locomotor rhythm / T cell differentiation / estrous cycle / BMP signaling pathway / response to glucose / regulation of neuron apoptotic process / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / Regulation of PTEN gene transcription / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / response to insulin / negative regulation of canonical Wnt signaling pathway / cellular response to gamma radiation / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Early growth response protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.412 Å
AuthorsWhite, M.A. / Zandarashvili, L. / Iwahara, J.
Citation
Journal: Febs Lett. / Year: 2015
Title: Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1.
Authors: Zandarashvili, L. / White, M.A. / Esadze, A. / Iwahara, J.
#1: Journal: Genes Dev. / Year: 2014
Title: Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.
Authors: Hashimoto, H. / Olanrewaju, Y.O. / Zheng, Y. / Wilson, G.G. / Zhang, X. / Cheng, X.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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 / struct_conn / struct_conn_type / struct_ref_seq
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 / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Early growth response protein 1
B: DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3')
C: DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*(5CM)P*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6846
Polymers17,4883
Non-polymers1963
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.009, 55.989, 128.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

-
Components

#1: Protein Early growth response protein 1 / EGR-1 / AT225 / Nerve growth factor-induced protein A / NGFI-A / Transcription factor ETR103 / ...EGR-1 / AT225 / Nerve growth factor-induced protein A / NGFI-A / Transcription factor ETR103 / Transcription factor Zif268 / Zinc finger protein 225 / Zinc finger protein Krox-24


Mass: 10722.302 Da / Num. of mol.: 1 / Fragment: UNP residues 335-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGR1, KROX24, ZNF225 / Production host: Escherichia coli (E. coli) / References: UniProt: P18146
#2: DNA chain DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3')


Mass: 3458.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*(5CM)P*GP*C)-3')


Mass: 3307.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 25mM BisTris pH8, 10% PEG-600, 450mM NaCl / PH range: 7-8

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2014
RadiationMonochromator: Si DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→43 Å / Num. obs: 29071 / % possible obs: 90.6 % / Redundancy: 15.4 % / Biso Wilson estimate: 10.75 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.036 / Rrim(I) all: 0.131 / Χ2: 1.321 / Net I/av σ(I): 30.828 / Net I/σ(I): 10.7 / Num. measured all: 447598
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.425.70.6537430.6710.2920.7190.39246
1.42-1.4560.5228470.7950.2270.5710.41354.4
1.45-1.486.10.4219690.8530.1810.460.4360.5
1.48-1.516.30.33210950.9040.1410.3620.41970.5
1.51-1.546.50.313180.9380.1260.3270.45182.8
1.54-1.5813.515700.5430.4840.47598.6
1.58-1.6215.615780.9010.3590.503100
1.62-1.6615.90.91315690.970.2390.9440.621100
1.66-1.7116.30.61316170.980.1620.6340.868100
1.71-1.76170.53815830.9850.1390.5560.906100
1.76-1.8318.10.45515760.9880.1120.4690.999100
1.83-1.918.30.36316090.9690.0890.3741.094100
1.9-1.9918.30.28715960.9920.070.2951.249100
1.99-2.0918.40.21516030.990.0520.2211.456100
2.09-2.2218.30.17716030.9670.0430.1821.743100
2.22-2.3918.40.14416030.9890.0350.1481.914100
2.39-2.6318.40.12216110.9870.0290.1262.101100
2.63-3.0218.10.1116350.9880.0260.1132.396100
3.02-3.8180.08616490.9880.0220.0892.217100
3.8-4316.70.06116970.9950.0150.0631.49797.2

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1810)refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb entry 4R2A

4r2a


Resolution: 1.412→27.357 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 3489 7.48 %Random
Rwork0.1717 ---
obs0.1738 46626 78.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.412→27.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms722 449 3 208 1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131283
X-RAY DIFFRACTIONf_angle_d1.3381827
X-RAY DIFFRACTIONf_dihedral_angle_d22.003505
X-RAY DIFFRACTIONf_chiral_restr0.071190
X-RAY DIFFRACTIONf_plane_restr0.032163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4119-1.43120.344130.305533X-RAY DIFFRACTION1
1.4312-1.45170.3119170.2704219X-RAY DIFFRACTION10
1.4517-1.47330.2572370.2539464X-RAY DIFFRACTION21
1.4733-1.49630.2765540.2466663X-RAY DIFFRACTION30
1.4963-1.52090.2356660.235816X-RAY DIFFRACTION37
1.5209-1.54710.256840.22561091X-RAY DIFFRACTION50
1.5471-1.57520.23461180.19661457X-RAY DIFFRACTION67
1.5752-1.60550.22351320.19041750X-RAY DIFFRACTION79
1.6055-1.63830.2021630.19211979X-RAY DIFFRACTION90
1.6383-1.67390.22281690.18472094X-RAY DIFFRACTION96
1.6739-1.71280.18081720.18712098X-RAY DIFFRACTION96
1.7128-1.75570.26721710.17492145X-RAY DIFFRACTION98
1.7557-1.80310.19981760.18012191X-RAY DIFFRACTION100
1.8031-1.85620.2311750.17662172X-RAY DIFFRACTION100
1.8562-1.91610.20331820.18242173X-RAY DIFFRACTION100
1.9161-1.98450.21081790.19052206X-RAY DIFFRACTION100
1.9845-2.0640.19081770.17522180X-RAY DIFFRACTION100
2.064-2.15790.20061790.17552175X-RAY DIFFRACTION100
2.1579-2.27160.18611780.16462200X-RAY DIFFRACTION100
2.2716-2.41380.1761770.16262181X-RAY DIFFRACTION100
2.4138-2.60010.21431750.17752183X-RAY DIFFRACTION100
2.6001-2.86150.21991760.18422183X-RAY DIFFRACTION100
2.8615-3.27490.22071810.17562213X-RAY DIFFRACTION100
3.2749-4.12380.17851710.14672145X-RAY DIFFRACTION99
4.1238-27.36240.16431770.14532126X-RAY DIFFRACTION97
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)
10.0059-0.00680.00630.0089-0.00860.0101-0.0244-0.02010.00940.03150.0029-0.00020.03820.0191-0.01070.2102-0.0224-0.03990.1615-0.01930.06616.4181-6.2665-3.4961
20.0011-0.00030.00130.000700.0018-0.0025-0.00240.0014-0.0037-0.01290.0056-0.0044-0.0047-00.2525-0.0512-0.01030.281-0.08270.147-5.528-2.5466-5.0991
30.0003-0.0005-0.00010.00110.00020.0005-0.00980.00660.01080.0104-0.0106-0.0052-0.0156-0.005600.1381-0.0398-0.00640.1949-0.0740.146-15.7982-1.6767-17.0065
40.0018-0.0001-0.00120.0089-0.00220.00290.0134-0.02050.0415-0.0069-0.0562-0.0088-0.0440.0681-0.00970.0907-0.02930.00130.1131-0.00480.0845-9.802-10.5535-24.3116
50.0004-0.0003-00.0009-0.00010.0008-0.00910.0117-0.00490.0114-0.0188-0.011-0.01520.0097-0.00190.0635-0.0113-00.1171-0.00060.073-7.3987-20.704-29.4115
60.0095-0.002-0.00690.0112-0.00020.0062-0.0033-0.0084-0.01050.0046-0.0137-0.00730.01110.01060.00120.05560.00350.03320.09040.0110.08-3.5278-30.2563-27.6462
70.0130.0035-0.00080.0016-0.00140.0018-0.0014-0.01-0.0115-0.0035-0.00560.01960.00370.0003-0.0110.1367-0.1482-0.00150.11640.00470.096-12.0992-17.7784-17.8239
80.000200.00190.0011-0.00180.0060.0079-0.0278-0.0256-0.0108-0.0013-0.02270.0149-0.01110.02540.1461-0.12920.01990.11110.03720.13655.8325-9.5535-16.1096
90.00340.00360.00110.0083-0.00360.0075-0.0112-0.00290.0118-0.003-0.01390.002-0.00860.0056-0.03370.1443-0.12850.00840.101-0.02150.11271.9398-5.6107-21.0824
100.01670.01070.00040.0121-0.00040.00040.002-0.0158-0.00180.0055-0.0056-0.0160.00390.0001-0.00480.1344-0.1056-0.01280.12010.0360.0946-3.4961-20.8602-13.7105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 102:125)
2X-RAY DIFFRACTION2(chain A and resid 126:133)
3X-RAY DIFFRACTION3(chain A and resid 134:143)
4X-RAY DIFFRACTION4(chain A and resid 144:166)
5X-RAY DIFFRACTION5(chain A and resid 167:178)
6X-RAY DIFFRACTION6(chain A and resid 179:187)
7X-RAY DIFFRACTION7(chain B and resid 1:5)
8X-RAY DIFFRACTION8(chain B and resid 6:11)
9X-RAY DIFFRACTION9(chain C and resid 51:56)
10X-RAY DIFFRACTION10(chain C and resid 57:61)

+
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