[English] 日本語
Yorodumi
- PDB-1guu: CRYSTAL STRUCTURE OF C-MYB R1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1guu
TitleCRYSTAL STRUCTURE OF C-MYB R1
ComponentsMYB PROTO-ONCOGENE PROTEIN
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / MYB / C-MYB / DNA BINDING / ION BINDI PROTO-ONCOGENE / NUCLEAR PROTEIN / ACTIVATOR
Function / homology
Function and homology information


myeloid cell development / embryonic digestive tract development / myeloid cell differentiation / stem cell division / cellular response to interleukin-6 / WD40-repeat domain binding / homeostasis of number of cells / spleen development / B cell differentiation / cellular response to leukemia inhibitory factor ...myeloid cell development / embryonic digestive tract development / myeloid cell differentiation / stem cell division / cellular response to interleukin-6 / WD40-repeat domain binding / homeostasis of number of cells / spleen development / B cell differentiation / cellular response to leukemia inhibitory factor / thymus development / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / calcium ion transport / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain ...Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator Myb
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTahirov, T.H. / Ogata, K.
Citation
Journal: To be Published
Title: Crystal Structure of C-Myb DNA-Binding Domain: Specific Na+ Binding and Correlation with NMR Structure
Authors: Tahirov, T.H. / Morii, H. / Uedaira, H. / Sasaki, M. / Sarai, A. / Adachi, S. / Park, S.Y. / Kamiya, N. / Ogata, K.
#1: Journal: Cell (Cambridge,Mass.) / Year: 2002
Title: Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter
Authors: Tahirov, T.H. / Sato, K. / Ichikawa-Iwata, E. / Sasaki, M. / Inoue-Bungo, T. / Shiina, M. / Kimura, K. / Takata, S. / Fujikawa, A. / Morii, H. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K.
History
DepositionJan 30, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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
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_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYB PROTO-ONCOGENE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3422
Polymers6,3191
Non-polymers231
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)26.273, 35.303, 24.039
Angle α, β, γ (deg.)90.00, 93.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein MYB PROTO-ONCOGENE PROTEIN / C-MYB


Mass: 6319.105 Da / Num. of mol.: 1 / Fragment: R1, RESIDUES 38-89 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P06876
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.76 Å3/Da / Density % sol: 30.16 %
Crystal growpH: 6.8
Details: 1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED TO PREVENT THE CRYSTAL CRACKING ...Details: 1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED TO PREVENT THE CRYSTAL CRACKING DURING THE FLASH COOLING

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 5574 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 2.959 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.653
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.43 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 2.279 / % possible all: 72.5

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MBE

1mbe


Resolution: 1.6→19.85 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 729344.03 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 306 5.5 %RANDOM
Rwork0.192 ---
obs0.192 5531 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5539 Å2 / ksol: 0.384404 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.44 Å20 Å2-3.84 Å2
2---4.79 Å20 Å2
3----1.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-20 Å
Luzzati sigma a0.16 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms433 0 1 42 476
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.841.5
X-RAY DIFFRACTIONc_mcangle_it2.862
X-RAY DIFFRACTIONc_scbond_it3.232
X-RAY DIFFRACTIONc_scangle_it4.982.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 35 4.6 %
Rwork0.272 724 -
obs--78.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

+
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