[English] 日本語
Yorodumi
- PDB-4auw: CRYSTAL STRUCTURE OF THE BZIP HOMODIMERIC MAFB IN COMPLEX WITH TH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4auw
TitleCRYSTAL STRUCTURE OF THE BZIP HOMODIMERIC MAFB IN COMPLEX WITH THE C- MARE BINDING SITE
Components
  • (C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')) x 2
  • TRANSCRIPTION FACTOR MAFB
KeywordsTRANSCRIPTION / DNA / MACROPHAGE
Function / homology
Function and homology information


rhombomere 6 development / abducens nerve formation / rhombomere 5 development / brain segmentation / cornified envelope assembly / regulation of myeloid cell differentiation / negative regulation of erythrocyte differentiation / segment specification / respiratory gaseous exchange by respiratory system / inner ear morphogenesis ...rhombomere 6 development / abducens nerve formation / rhombomere 5 development / brain segmentation / cornified envelope assembly / regulation of myeloid cell differentiation / negative regulation of erythrocyte differentiation / segment specification / respiratory gaseous exchange by respiratory system / inner ear morphogenesis / negative regulation of osteoclast differentiation / keratinocyte differentiation / thymus development / protein processing / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / gene expression / T cell differentiation in thymus / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein-containing complex binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Maf transcription factor, N-terminal / Maf N-terminal region / Transcription factor Maf family / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily ...Maf transcription factor, N-terminal / Maf N-terminal region / Transcription factor Maf family / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / : / DNA / DNA (> 10) / Transcription factor MafB
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.9 Å
AuthorsTextor, L.C. / Holton, S. / Wilmanns, M.
CitationJournal: Acta Crystallogr Sect F Struct Biol Cryst Commun. / Year: 2007
Title: Expression, purification, crystallization and preliminary crystallographic analysis of the mouse transcription factor MafB in complex with its DNA-recognition motif Cmare
Authors: Textor, L.C. / Wilmanns, M. / Holton, S.J.
History
DepositionMay 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / reflns / reflns_shell
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_beamline / _reflns.pdbx_Rsym_value
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_asym_id / _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_asym_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 / _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_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_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: TRANSCRIPTION FACTOR MAFB
B: TRANSCRIPTION FACTOR MAFB
C: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
D: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
E: TRANSCRIPTION FACTOR MAFB
F: TRANSCRIPTION FACTOR MAFB
G: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
H: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,88413
Polymers71,9288
Non-polymers9575
Water00
1
A: TRANSCRIPTION FACTOR MAFB
B: TRANSCRIPTION FACTOR MAFB
C: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
D: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5197
Polymers35,9644
Non-polymers5553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-114.2 kcal/mol
Surface area18650 Å2
MethodPISA
2
E: TRANSCRIPTION FACTOR MAFB
F: TRANSCRIPTION FACTOR MAFB
G: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
H: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3656
Polymers35,9644
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-107.5 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.964, 94.964, 200.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
TRANSCRIPTION FACTOR MAFB / MAF-B / KREISLER / SEGMENTATION PROTEIN KR / TRANSCRIPTION FACTOR MAF-1 / V-MAF MUSCULOAPONEUROTIC ...MAF-B / KREISLER / SEGMENTATION PROTEIN KR / TRANSCRIPTION FACTOR MAF-1 / V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG B


Mass: 11540.252 Da / Num. of mol.: 4 / Fragment: RESIDUES 211-305 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P54841
#2: DNA chain C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')


Mass: 6437.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')


Mass: 6446.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.44 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Type: ESRF / Wavelength: 0.9535
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.9→48 Å / Num. obs: 20968 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Rsym value: 0.083 / Net I/σ(I): 7
Reflection shellResolution: 2.9→3.06 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.218 / % possible all: 100

-
Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.9→85.75 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.888 / SU B: 16.896 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 0.69 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29047 1081 5.1 %RANDOM
Rwork0.25505 ---
obs0.25684 19927 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.9→85.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 1710 12 0 4660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1472.4046909
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.015349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62823.136169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71115643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9341544
X-RAY DIFFRACTIONr_chiral_restr0.0550.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023094
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 81 -
Rwork0.492 1450 -
obs--100 %

+
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