[English] 日本語
Yorodumi
- PDB-4jol: Complex structure of AML1-ETO NHR2 domain with HEB fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jol
TitleComplex structure of AML1-ETO NHR2 domain with HEB fragment
Components
  • Protein CBFA2T1
  • Transcription factor 12
KeywordsDNA BINDING PROTEIN / leukemia / AML1-ETO / HEB / NHR2 domain
Function / homology
Function and homology information


response to gonadotropin-releasing hormone / cAMP response element binding / HMG box domain binding / bHLH transcription factor binding / NGF-stimulated transcription / muscle organ development / negative regulation of fat cell differentiation / Myogenesis / E-box binding / SMAD binding ...response to gonadotropin-releasing hormone / cAMP response element binding / HMG box domain binding / bHLH transcription factor binding / NGF-stimulated transcription / muscle organ development / negative regulation of fat cell differentiation / Myogenesis / E-box binding / SMAD binding / cis-regulatory region sequence-specific DNA binding / positive regulation of neuron differentiation / nuclear matrix / RNA polymerase II transcription regulator complex / transcription corepressor activity / sequence-specific double-stranded DNA binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / immune response / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #230 / Protein CBFA2T1 / CBFA2T family / NHR2-like / NHR2 domain like / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #230 / Protein CBFA2T1 / CBFA2T family / NHR2-like / NHR2 domain like / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Helix-loop-helix DNA-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix non-globular / Special
Similarity search - Domain/homology
Protein CBFA2T1 / Transcription factor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.906 Å
AuthorsWang, Z. / Patel, D.J.
CitationJournal: Nature / Year: 2013
Title: A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis.
Authors: Sun, X.J. / Wang, Z. / Wang, L. / Jiang, Y. / Kost, N. / Soong, T.D. / Chen, W.Y. / Tang, Z. / Nakadai, T. / Elemento, O. / Fischle, W. / Melnick, A. / Patel, D.J. / Nimer, S.D. / Roeder, R.G.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Aug 28, 2013Group: Database references
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein CBFA2T1
B: Protein CBFA2T1
C: Protein CBFA2T1
D: Protein CBFA2T1
E: Transcription factor 12
F: Transcription factor 12
G: Transcription factor 12
H: Transcription factor 12


Theoretical massNumber of molelcules
Total (without water)42,6328
Polymers42,6328
Non-polymers00
Water00
1
A: Protein CBFA2T1
C: Protein CBFA2T1
E: Transcription factor 12
G: Transcription factor 12


Theoretical massNumber of molelcules
Total (without water)21,3164
Polymers21,3164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-47 kcal/mol
Surface area11140 Å2
MethodPISA
2
B: Protein CBFA2T1
D: Protein CBFA2T1
F: Transcription factor 12
H: Transcription factor 12


Theoretical massNumber of molelcules
Total (without water)21,3164
Polymers21,3164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-48 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.485, 139.485, 43.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
Protein CBFA2T1 / Cyclin-D-related protein / Eight twenty one protein / Protein ETO / Protein MTG8 / Zinc finger MYND ...Cyclin-D-related protein / Eight twenty one protein / Protein ETO / Protein MTG8 / Zinc finger MYND domain-containing protein 2


Mass: 8036.026 Da / Num. of mol.: 4 / Fragment: NHR2 domain of AML1-ETO (unp residues 338-400)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUNX1T1, AML1T1, CBFA2T1, CDR, ETO, MTG8, ZMYND2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06455
#2: Protein/peptide
Transcription factor 12 / TCF-12 / Class B basic helix-loop-helix protein 20 / bHLHb20 / DNA-binding protein HTF4 / E-box- ...TCF-12 / Class B basic helix-loop-helix protein 20 / bHLHb20 / DNA-binding protein HTF4 / E-box-binding protein / Transcription factor HTF-4


Mass: 2622.069 Da / Num. of mol.: 4 / Fragment: A fragment of HEB (unp residues 177-200)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCF12, BHLHB20, HEB, HTF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99081

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.69 Å3/Da / Density % sol: 78.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 mM Tris, 20% ETHANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 197 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2000
RadiationMonochromator: SI mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 20470 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rsym value: 0.072 / Net I/σ(I): 47.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2035 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WQ6

1wq6


Resolution: 2.906→27.127 Å / SU ML: 1 / σ(F): 1.97 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 2007 9.83 %Random
Rwork0.2071 ---
obs0.2115 20410 98.78 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.752 Å2 / ksol: 0.298 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.4025 Å2-0 Å2-0 Å2
2--6.4025 Å2-0 Å2
3----12.8049 Å2
Refinement stepCycle: LAST / Resolution: 2.906→27.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 0 0 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092477
X-RAY DIFFRACTIONf_angle_d1.3533347
X-RAY DIFFRACTIONf_dihedral_angle_d21.399949
X-RAY DIFFRACTIONf_chiral_restr0.089353
X-RAY DIFFRACTIONf_plane_restr0.006429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9062-2.97880.42181480.37891317X-RAY DIFFRACTION99
2.9788-3.05920.31791500.30471337X-RAY DIFFRACTION100
3.0592-3.14910.41271450.30741292X-RAY DIFFRACTION99
3.1491-3.25060.34321400.29571319X-RAY DIFFRACTION100
3.2506-3.36650.36461500.26151349X-RAY DIFFRACTION100
3.3665-3.50110.25341430.20261326X-RAY DIFFRACTION100
3.5011-3.66010.27261450.20341355X-RAY DIFFRACTION100
3.6601-3.85250.23611440.19791313X-RAY DIFFRACTION100
3.8525-4.09310.23321520.18391322X-RAY DIFFRACTION100
4.0931-4.40790.18041390.16361325X-RAY DIFFRACTION100
4.4079-4.84920.21121460.15611347X-RAY DIFFRACTION100
4.8492-5.54570.19381440.19421310X-RAY DIFFRACTION99
5.5457-6.96740.28911350.21141335X-RAY DIFFRACTION100
6.9674-27.12770.26181260.21851156X-RAY DIFFRACTION87
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)
19.23655.4526-0.13724.5265-0.47310.33861.2942-1.0248-1.40410.9984-0.9974-0.91070.2066-0.0034-0.34880.671-0.0825-0.02710.5870.05120.567229.6811-67.3878.7768
28.21993.362-0.0442.336-0.00870.7023-0.14321.8542-1.76050.16370.5196-0.8190.04870.0753-0.32430.55110.00890.03960.7349-0.09530.623843.5484-59.328-0.7316
38.78513.74120.86053.02070.82670.57341.497-0.64960.98121.1519-0.87420.539-0.64260.1249-0.33220.637-0.01090.05220.59290.01030.362440.2923-52.07826.7541
46.90963.50481.29833.25471.05530.42010.58570.92331.10340.64220.0340.6247-0.2242-0.3579-0.35250.51420.0382-0.01780.58850.08470.404625.0205-60.97051.3308
56.3666-1.2998-4.27564.6859-4.04198.32671.5718-0.15110.02571.1369-0.15650.6985-0.14290.4881-0.95650.596-0.1645-0.32681.080.28260.990626.0962-70.717617.5629
64.621-0.95812.45172.88670.762.1123-0.56261.1782-0.1107-0.24750.07920.1644-0.7382-0.0070.1590.79120.11410.02870.87910.34940.936118.7476-63.0527-6.2007
73.04260.50060.62437.62370.03243.17470.7813-0.4834-0.6890.5656-1.17910.6012-0.5794-0.84710.3780.75170.04630.42560.7307-0.04091.160345.4589-47.715714.3169
80.09-0.55330.72533.1631-3.60265.1462-0.73462.1621-2.70970.63210.2079-0.2791-1.3173-0.93280.08780.5563-0.28950.26821.3765-0.69921.210649.2337-57.8201-9.7461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'
7X-RAY DIFFRACTION7chain 'G'
8X-RAY DIFFRACTION8chain 'H'

+
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://pdbjlvh1.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