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- PDB-6dmx: HBZ56 in complex with KIX and c-Myb -

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Basic information

Entry
Database: PDB / ID: 6dmx
TitleHBZ56 in complex with KIX and c-Myb
Components
  • BZIP factor
  • CREB-binding protein
  • Transcriptional activator Myb
KeywordsTRANSCRIPTION / transcription coactivator / transcription factor / viral / eukaryotic / complex
Function / homology
Function and homology information


Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / myeloid cell development / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Regulation of gene expression by Hypoxia-inducible Factor / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Formation of the beta-catenin:TCF transactivating complex ...Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / myeloid cell development / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Regulation of gene expression by Hypoxia-inducible Factor / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / cAMP response element binding protein binding / Notch-HLH transcription pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / germ-line stem cell population maintenance / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / embryonic digestive tract development / Estrogen-dependent gene expression / CD209 (DC-SIGN) signaling / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / myeloid cell differentiation / negative regulation of interferon-beta production / stem cell division / cellular response to interleukin-6 / N-terminal peptidyl-lysine acetylation / MRF binding / face morphogenesis / negative regulation of transcription by RNA polymerase I / WD40-repeat domain binding / protein-lysine-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / histone acetyltransferase activity / acetyltransferase activity / TFIIB-class transcription factor binding / histone acetyltransferase complex / homeostasis of number of cells / viral process / positive regulation of double-strand break repair via homologous recombination / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / spleen development / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / B cell differentiation / cellular response to leukemia inhibitory factor / positive regulation of DNA-binding transcription factor activity / thymus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein destabilization / PML body / cellular response to virus / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / calcium ion transport / disordered domain specific binding / cellular response to UV / rhythmic process / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / molecular adaptor activity / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / damaged DNA binding / transcription coactivator activity / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / host cell nucleus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
HTLV-1 basic zipper factor / Coactivator CBP, KIX domain / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding ...HTLV-1 basic zipper factor / Coactivator CBP, KIX domain / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Myb-type HTH DNA-binding domain profile. / Serum Albumin; Chain A, Domain 1 / Zinc finger ZZ-type signature. / Myb domain / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Nuclear receptor coactivator, interlocking / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator Myb / HTLV-1 basic zipper factor / Histone lysine acetyltransferase CREBBP / BZIP factor
Similarity search - Component
Biological speciesHuman T-lymphotropic virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYang, K. / Wright, P.E. / Stanfield, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)CA214054 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for cooperative regulation of KIX-mediated transcription pathways by the HTLV-1 HBZ activation domain.
Authors: Yang, K. / Stanfield, R.L. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: BZIP factor
C: Transcriptional activator Myb
D: CREB-binding protein
A: Transcriptional activator Myb
B: CREB-binding protein
J: BZIP factor
H: Transcriptional activator Myb
I: CREB-binding protein
F: Transcriptional activator Myb
G: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)69,78110
Polymers69,78110
Non-polymers00
Water00
1
E: BZIP factor
C: Transcriptional activator Myb
D: CREB-binding protein
A: Transcriptional activator Myb
B: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)34,8915
Polymers34,8915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-36 kcal/mol
Surface area16070 Å2
MethodPISA
2
J: BZIP factor
H: Transcriptional activator Myb
I: CREB-binding protein
F: Transcriptional activator Myb
G: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)34,8915
Polymers34,8915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-35 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.997, 80.311, 64.641
Angle α, β, γ (deg.)90.00, 92.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21J
12C
22A
13C
23H
14C
24F
15D
25B
16D
26I
17D
27G
18A
28H
19A
29F
110B
210I
111B
211G
112H
212F
113I
213G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLUEA16 - 5318 - 55
21GLUGLUGLUGLUJF16 - 5318 - 55
12ASPASPGLUGLUCB288 - 3085 - 25
22ASPASPGLUGLUAD288 - 3085 - 25
13ASPASPGLUGLUCB288 - 3085 - 25
23ASPASPGLUGLUHG288 - 3085 - 25
14ASPASPGLUGLUCB288 - 3085 - 25
24ASPASPGLUGLUFI288 - 3085 - 25
15TRPTRPSERSERDC591 - 6707 - 86
25TRPTRPSERSERBE591 - 6707 - 86
16TRPTRPARGARGDC591 - 6717 - 87
26TRPTRPARGARGIH591 - 6717 - 87
17TRPTRPSERSERDC591 - 6707 - 86
27TRPTRPSERSERGJ591 - 6707 - 86
18GLUGLUGLUGLUAD287 - 3084 - 25
28GLUGLUGLUGLUHG287 - 3084 - 25
19ASPASPGLUGLUAD288 - 3085 - 25
29ASPASPGLUGLUFI288 - 3085 - 25
110TRPTRPSERSERBE591 - 6707 - 86
210TRPTRPSERSERIH591 - 6707 - 86
111LYSLYSLEULEUBE589 - 6725 - 88
211LYSLYSLEULEUGJ589 - 6725 - 88
112ASPASPGLUGLUHG288 - 3085 - 25
212ASPASPGLUGLUFI288 - 3085 - 25
113TRPTRPSERSERIH591 - 6707 - 86
213TRPTRPSERSERGJ591 - 6707 - 86

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13

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Components

#1: Protein BZIP factor


Mass: 6300.014 Da / Num. of mol.: 2 / Fragment: residues 3-56 / Mutation: C9A, C14A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-lymphotropic virus 1 / Gene: HBZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q2Q067, UniProt: P0C746*PLUS
#2: Protein/peptide
Transcriptional activator Myb / Proto-oncogene c-Myb


Mass: 3810.263 Da / Num. of mol.: 4 / Fragment: residues 284-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myb / Production host: Escherichia coli (E. coli) / References: UniProt: P06876
#3: Protein
CREB-binding protein


Mass: 10485.053 Da / Num. of mol.: 4 / Fragment: residues 284-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crebbp, Cbp / Production host: Escherichia coli (E. coli) / References: UniProt: P45481, histone acetyltransferase

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13196 / % possible obs: 95.2 % / Redundancy: 6 % / Net I/σ(I): 16.6
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AGH

2agh


Resolution: 2.8→40.97 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / SU B: 30.023 / SU ML: 0.546 / Cross valid method: THROUGHOUT / ESU R Free: 0.505 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30083 660 5 %RANDOM
Rwork0.23871 ---
obs0.24198 12521 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 94.383 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20.3 Å2
2--4.76 Å20 Å2
3----3.07 Å2
Refinement stepCycle: 1 / Resolution: 2.8→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 0 0 4187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0154244
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173950
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.7375685
X-RAY DIFFRACTIONr_angle_other_deg0.411.7059312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8415495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.66116.963135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30515671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.251532
X-RAY DIFFRACTIONr_chiral_restr0.0390.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
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_it6.0919.4632013
X-RAY DIFFRACTIONr_mcbond_other6.0899.4632014
X-RAY DIFFRACTIONr_mcangle_it9.58714.1722497
X-RAY DIFFRACTIONr_mcangle_other9.58514.1722498
X-RAY DIFFRACTIONr_scbond_it6.44810.0892231
X-RAY DIFFRACTIONr_scbond_other6.44710.0892232
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.49914.9253189
X-RAY DIFFRACTIONr_long_range_B_refined14.6124921
X-RAY DIFFRACTIONr_long_range_B_other14.6114922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11E10930.11
12J10930.11
21C5840.12
22A5840.12
31C5840.1
32H5840.1
41C5720.11
42F5720.11
51D26200.1
52B26200.1
61D25820.09
62I25820.09
71D25120.11
72G25120.11
81A6210.1
82H6210.1
91A5720.12
92F5720.12
101B25110.12
102I25110.12
111B27050.07
112G27050.07
121H5640.14
122F5640.14
131I24080.12
132G24080.12
LS refinement shellResolution: 2.802→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 53 -
Rwork0.424 824 -
obs--84.73 %

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