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- PDB-7psx: Structure of HOXB13 bound to hydroxymethylated DNA -

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Basic information

Entry
Database: PDB / ID: 7psx
TitleStructure of HOXB13 bound to hydroxymethylated DNA
Components
  • DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
  • Homeobox protein Hox-B13
KeywordsDNA BINDING PROTEIN / transcription / hydroxymethylation / protein-DNA complex / transcription factor
Function / homology
Function and homology information


epithelial cell maturation involved in prostate gland development / methyl-CpG binding / regulation of growth / response to testosterone / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epidermis development / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / sequence-specific double-stranded DNA binding / angiogenesis ...epithelial cell maturation involved in prostate gland development / methyl-CpG binding / regulation of growth / response to testosterone / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epidermis development / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / sequence-specific double-stranded DNA binding / angiogenesis / 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 / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Homeobox protein Hox1A3 N-terminal / Hox protein A13 N terminal / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein Hox-B13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMorgunova, E. / Popov, A. / Yin, Y. / Taipale, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of HOXB13 bound to hydroxymethylated DNA
Authors: Morgunova, E. / Popov, A. / Yin, Y. / Taipale, J.
History
DepositionSep 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
A: Homeobox protein Hox-B13
C: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
B: Homeobox protein Hox-B13
D: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
E: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
G: Homeobox protein Hox-B13
H: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
I: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
J: Homeobox protein Hox-B13
K: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,93614
Polymers73,88812
Non-polymers492
Water6,413356
1
A: Homeobox protein Hox-B13
C: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4964
Polymers18,4723
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-24 kcal/mol
Surface area10100 Å2
MethodPISA
2
B: Homeobox protein Hox-B13
D: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
E: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4964
Polymers18,4723
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-19 kcal/mol
Surface area10060 Å2
MethodPISA
3
G: Homeobox protein Hox-B13
H: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
I: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,4723
Polymers18,4723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-19 kcal/mol
Surface area10110 Å2
MethodPISA
4
J: Homeobox protein Hox-B13
K: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,4723
Polymers18,4723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-18 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.153, 55.541, 101.080
Angle α, β, γ (deg.)88.020, 81.460, 84.940
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22G
13A
23J
14C
24D
15C
25H
16C
26K
17F
27E
18F
28I
19F
29L
110B
210G
111B
211J
112D
212H
113D
213K
114E
214I
115E
215L
116G
216J
117H
217K
118I
218L

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSALAALAAA218 - 2762 - 60
21LYSLYSALAALABD218 - 2762 - 60
12ARGARGLEULEUAA217 - 2751 - 59
22ARGARGLEULEUGG217 - 2751 - 59
13LYSLYSVALVALAA218 - 2742 - 58
23LYSLYSVALVALJJ218 - 2742 - 58
14DTDTDCDCCB1 - 181 - 18
24DTDTDCDCDE1 - 181 - 18
15DTDTDCDCCB1 - 181 - 18
25DTDTDCDCHH1 - 181 - 18
16DTDTDCDCCB1 - 181 - 18
26DTDTDCDCKK1 - 181 - 18
17DGDGDADAFC1 - 181 - 18
27DGDGDADAEF1 - 181 - 18
18DGDGDADAFC1 - 181 - 18
28DGDGDADAII1 - 181 - 18
19DGDGDADAFC1 - 181 - 18
29DGDGDADALL1 - 181 - 18
110LYSLYSLEULEUBD218 - 2752 - 59
210LYSLYSLEULEUGG218 - 2752 - 59
111LYSLYSVALVALBD218 - 2742 - 58
211LYSLYSVALVALJJ218 - 2742 - 58
112DTDTDCDCDE1 - 181 - 18
212DTDTDCDCHH1 - 181 - 18
113DTDTDCDCDE1 - 181 - 18
213DTDTDCDCKK1 - 181 - 18
114DGDGDADAEF1 - 181 - 18
214DGDGDADAII1 - 181 - 18
115DGDGDADAEF1 - 181 - 18
215DGDGDADALL1 - 181 - 18
116LYSLYSVALVALGG218 - 2742 - 58
216LYSLYSVALVALJJ218 - 2742 - 58
117DTDTDCDCHH1 - 181 - 18
217DTDTDCDCKK1 - 181 - 18
118DGDGDADAII1 - 181 - 18
218DGDGDADALL1 - 181 - 18

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

#1: Protein
Homeobox protein Hox-B13 /


Mass: 7411.749 Da / Num. of mol.: 4 / Fragment: UNP residues 217-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOXB13 / Plasmid: pETG20A-SBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92826
#2: DNA chain
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')


Mass: 5543.584 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Mass: 5516.636 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 27% PEG 1000, 8% PEG 200, 0.15M KCl, 0.1M MgCl2, 0.05M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.97→48.85 Å / Num. obs: 55783 / % possible obs: 97.2 % / Redundancy: 4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.284 / Rpim(I) all: 0.158 / Rrim(I) all: 0.326 / Net I/σ(I): 2.4 / Num. measured all: 222658 / Scaling rejects: 66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.97-2.023.25.7761014231470.0743.7286.9220.377.7
9.05-48.854.10.16223405750.9810.0860.1846.497.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.47 Å47.95 Å
Translation3.47 Å47.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EDN

5edn


Resolution: 2→47 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.008 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 1603 2.9 %RANDOM
Rwork0.2601 ---
obs0.2608 52887 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200.9 Å2 / Biso mean: 40.422 Å2 / Biso min: 13.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å2-0.63 Å22.26 Å2
2---1.05 Å2-0.69 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 2→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 2968 2 356 5365
Biso mean--46.92 36.34 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125422
X-RAY DIFFRACTIONr_bond_other_d0.0020.0193826
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.3857895
X-RAY DIFFRACTIONr_angle_other_deg1.4482.2078948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1915247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70618.201139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.01115489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0231536
X-RAY DIFFRACTIONr_chiral_restr0.0760.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021191
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A19620.07
12B19620.07
21A19580.08
22G19580.08
31A19210.07
32J19210.07
41C15220.08
42D15220.08
51C15360.06
52H15360.06
61C15320.06
62K15320.06
71F15610.02
72E15610.02
81F15660.03
82I15660.03
91F15580.03
92L15580.03
101B20160.07
102G20160.07
111B19980.06
112J19980.06
121D15870.05
122H15870.05
131D15730.05
132K15730.05
141E15620.03
142I15620.03
151E15560.03
152L15560.03
161G20120.07
162J20120.07
171H15840.02
172K15840.02
181I15640.05
182L15640.05
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 103 -
Rwork0.409 3881 -
all-3984 -
obs--97.67 %

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